"Subtract" is the word.
Though the obsolete word "substract" did exist, any occurrence you see these days is most likely just a common mistake, formed by analogy either with "abstract" or with other languages whose corresponding words do have two ‘s’s.
Many recent dictionaries do not list "substract".
Of "substract", the Century Dictionary (1891) said : An erroneous form of subtract , common in vulgar use.
Webster's Revised Unabridged Dictionary of 1913 called it "obsolete", while the even older version of 1828 said Note.--Substract was formerly used in analogy with abstract.
But in modern usage, it is written according to the Latin, subtract.
See this word and its derivatives.
Additionally, I know people who find "substract" very annoying. :-)
english.stackexchange.com/users/77/ShreevatsaR
It seems that the usage of "substract" is linguistically incorrect.
However, I disagree about explaining this usage as a "showing-off".
It seems that other languages do contain the letter "s" as in "soustraction" in French.
People with a multi-lingual background are more likely to make mistakes, and it is nice if we just point that out to them without prejudice.
english.stackexchange.com/users/26538/Aly
French people use "substract" mistakingly a lot because in french, the word is "soustraction", which contains the sound "s" inside.
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If sub s tract is incorrect according to established English usage, this is only because English usage derives this verb from Latin subtraho ‘to subtract’, which excludes the ‑s‑ .
In many a Romance language — for example, in Spanish — it derives from the Latin prefix
sub‑ coupled with the Latin verb extraho ‘to extract’; hence Spanish sub s traer .
You say ‘sub-tract’ in English where in Spanish we say ‘sub-
ex tract’ ; hence the extra s .
Substract is incorrect in English, but it could equally have been correct if imported differently.
english.stackexchange.com/users/46645/Moisés Ramírez
I've never heard of "substract" and, more to the point, neither has my edition of the Oxford English Dictionary.
Even if it is a word, assuming that it means the same as "subtract" I can't see any point in preferring it over the better known word, apart from showing off.
english.stackexchange.com/users/1402/gkrogers
I found the word "substract" in a memoir written by an old Boston lady in the 1920s, describing how she as a child (during the 1850s) pilfered newspapers from her mother's cache and was able to trade them for candy.
I like this usage, as it conveys a kind of arch, sneaky tone better than either "extract" or "subtract"
But it's not mathematical at all.
english.stackexchange.com/users/23634/Jane
By looking at the etymology, we can see that "substract" is erroneous.
"subtract" is derived from a the Latin compound verb "subtraho", whose supine is "subtractum".
There is no form "substraho" of this verb.
english.stackexchange.com/users/23962/JamesHH
I read an article recently where the author used "substract" instead of "subtract".  I'm more familiar with the latter word but after doing a bit of googling, it seems that both words are being used, although "subtract" seems more mainstream than the other. Which of the two is more appropriate? Is "substract" even acceptable?
Is "substract" (versus "subtract") a proper word?
english.stackexchange.com
<word-choice><errors>
english.stackexchange.com/questions/3640
english.stackexchange.com/users/1269/Jonn
"Substract" is linguistically incorrect and many recent dictionaries do not list it. It may have existed in the past, but any occurrence you see these is most likely a common mistake, and there is no obvious reason to prefer it over the better known word, "subtract". The verb subtract derives from Latin "subtraho". "Substract" is incorrect in English and is not in the Oxford English Dictionary, although the word has been found to be used in literature in the 1920s. Etymologically, "substract" is incorrect as the Latin compound verb is "subtraho" 
"Substract" is linguistically incorrect and many recent dictionaries do not list it. It may have existed in the past, but any occurrence you see these is most likely a common mistake, and there is no obvious reason to prefer it over the better known word, "subtract". "Subtract" is the correct word. The obsolete word "substract"  did  exist at one time though, but the usage of "substract" is linguistically incorrect and it is not listed in current dictionaries.
Though the obsolete word "substract"  did  exist, any occurrence you see these days is most likely just a common mistake. Many recent dictionaries do not list "substract". "Substract" is incorrect English and does not appear in the dictionary. It may have existed in the past, but it is certainly not used any longer and there is no obvious reason to opt for it over "subtract".
"Substract" has been used in writings to designate "remove"
"Subtract" is the correct word. The obsolete word "substract"  did  exist at one time though. The usage of "substract" is linguistically incorrect and it is not listed in current dictionaries.
"Substract" does not exist in the dictionary and is incorrect English. The word "substract" may have existed in the past, but it is no longer used. There is no clear reason to use "substract" over "subtract".