Pyrite FeS2 decorated sulfur-doped carbon (FeS2@S-C) fibers have been successfully synthesized by a facile bio-templating method and applied as the anode material for lithium ion batteries (LIBs). Cotton was used as both the carbon source and the template. SEM and TEM results showed that the FeS2 nanoparticles fabricated using 0.2M FeSO4 were uniformly embedded in or attached on the surface of the carbon fibers. FeS2@S-C synthesized with 0.2M FeSO4 showed the best cycle stability and rate capability, which retained a high reversible specific capacity of 689mAhg−1 after 100 cycles. The specific capacities are about 1200, 900, 700, 550 and 400mAhg−1 after every 10 cycles at 0.1, 0.2, 0.5, 1 and 2Ag−1. The excellent electrochemical performance can be ascribed to the highly conductive sulfur-doped carbon and the homogeneous distribution of FeS2 nanoparticles. It is believed that the S-doped carbon matrix acts as an effective buffer layer helping relieve the volume strain as well as a hinder preventing FeS2 from aggregating during cycling, which ensure the high electrochemical performance. This kind of low-cost anode with high specific capacity and improved cycling stability show potential application for high capacity lithium-ion batteries.