Some 3,740 people died until 23 October, a number that is set to rise as the two worst months are yet to come. Last year's death toll was 3,771.
This comes despite a sharp decline on the number of people crossing the Mediterranean this year.
The UN believes smugglers are changing their tactics, using riskier routes.
One of every 47 migrants or refugees attempting the voyage between Libya and Italy is dying, said William Spindler, spokesman for the UN High Commissioner for Refugees.
"This is by far the worse we ever have seen in the Mediterranean," he told journalists in Geneva.
"We can say the death rate has increased threefold."
There were 327,800 crossings this year, against more than one million in 2015, UN numbers showed.
Smugglers, the UN says, are organising more crossings in very bad weather and staging mass embarkations, in which thousands of people in flimsy boats set off at the same time.
This means that if they do run into trouble, rescue services cannot possibly save them all.
"Smuggling has become a big business, it's being done almost on an industrial scale," Mr Splinder added.
"So now they send several boats at the same time and that puts rescue services in difficulty because they need to rescue several thousand people on several hundred boats," he said.
An agreement between Turkey and the European Union to halt migrants from travelling to Greek islands has drastically reduced the number of boat arrivals there.
But there has been a traffic increase on the highly perilous journey between North Africa and Italy.
On Monday, the Italian coastguard said it recovered the bodies of 16 people during 21 rescue missions. Some 2,200 migrants were saved from 18 rubber boats.
This year is set to be the deadliest for migrants and refugees crossing the Mediterranean to Europe, the UN refugee agency says.