Iron disulfide (FeS2) powders were successfully synthesized by hydrothermal method. Cetyltrimethylammonium bromide (CTAB) had a great influence on the morphology, particle size, and electrochemical performance of the FeS2 powders. The as-synthesized FeS2 particles with CTAB had diameters of 2–4 μm and showed a sphere-like structure with sawtooth, while the counterpart prepared without CTAB exhibited irregular morphology with diameters in the range of 0.1–0.4 μm. As anode materials for Li-ion batteries, their electrochemical performances were investigated by galvanostatic charge–discharge test and electrochemical impedance spectrum. The FeS2 powder synthesized with CTAB can sustain 459 and 413 mAh g−1 at 89 and 445 mA g−1 after 35 cycles, respectively, much higher than those prepared without CTAB (411 and 316 mAh g−1). The enhanced rate capability and cycling stability were attributed to the less-hindered surface layer and better electrical contact from the sawtooth-like surface and micro-sized sphere morphology, which led to enhanced process kinetics.