As a pseudocapacitive electrode materials for supercapacitor, Polypyrrole (PPy) exhibit excellent theoretical specific capacitance. However, it suffers from a poor cycling stability due to structural instability during charge-discharge process. In this work, a novel and facile hydrothermal method has been developed for the intercalation composites of PPy/MoS2 with multilayer three-dimensional structure. The report result shows that the as-prepared electrode possess a outstanding electrochemical properties with significantly specific capacitance of 895.6Fg−1 at current density of 1Ag−1, higher energy density (3.774Whkg−1) at power density of 252.8kWkg−1, furthermore, it also achieve remarkable cycling stability (~98% capacitance retention after 10,000 cycles) which is attributed to the synergistic effect of PPy and MoS2. This synthetic strategy integrates performance enables the multilayer PPy/MoS2 composites to be a promising electrode for energy storage applications.