Carbon-coated layer on silicon nanoparticles (SiNPs) can improve the conductivity of SiNPs and affect the cycle performance of SiNPs based anode in lithium ion batteries. SiNPs coated with three different type of carbon (amorphous carbon, order carbon, amorphous/ordered dual carbon) are prepared and their electrochemical properties are investigated. Amorphous carbon (AC) coating shows a better conductivity, while the ordered carbon (OC) coating presents a good volume variation tolerance. Interestingly, amorphous/ordered dual carbon (AC/OC) coating structure simultaneously has the two advantages that amorphous and ordered carbons coating structures have. Hence, as an anode material in lithium ion batteries, AC/OC-coated SiNPs demonstrates an eclectic initial discharge capacity of 3300 mAhg−1 and exhibits an enhanced cycle performance that remains a discharge specific capacity of 1020 mAhg−1 at 200 cycles as well as 650 mAhg−1 after 500 cycles at the current density of 0.36 Ag−1 in the voltage range of 0.01–1.5 V. The preparation procedure of SiNPs@AC/OC is easy for large scale production and SiNPs@AC/OC can be mixed with graphite as composite anode materials for lithium ion batteries in industrial application.