Transition metal dichalcogenides represented by molybdenum disulfide (MoS2) have attracted worldwide attention due to their high specific capacity originating from the four-electron transfer reaction for lithium-ion batteries. Here, one nanoflower-like MoS2 with high specific surface area and more active sites is synthesized by a facile and effective hydrothermal method with cetyltrimethylammonium bromide (CTAB) as the surfactant. To improve the conductivity and structural stability of MoS2, Co doping and polyaniline (PANI) surface modification are carried out in sequence, and the obtained MoS2@Co/PANI hybrid materials show the improved electrochemical performance. In particular, the optimal hybrid material with 15 wt% PANI can exhibit a high discharge specific capacity of 1429.7 mAh·g−1 at 200 mA·g−1, and deliver a reversible capacity of 649.4 mAh·g−1 after 100 cycles. The excellent cycling and rate performances of MoS2@Co/PANI hybrid materials can be attributed to the enhanced conductivity resulting from the synthetic role of Co doping and PANI surface modification. One rational design is also offered to improve the electrochemical performance of functionalized electrode materials in lithium-ion batteries.