Confinement transition metal compounds with conducting polymer is an effectively to inhibit the volume change during the Faradic reaction. In this work, three-dimensional flower-like polypyrrole-wrapped ZnCo2S4 (ZnCo2S4@PPy) core-shell nanoclusters were successfully prepared by two-step hydrothermal and electrochemical deposition methods. The obtained ZnCo2S4@PPy composite exhibited remarkable electrochemical performance corresponding to a specific capacitance of 1486 F g−1 at 1 A g−1, which suggested its potential use as a supercapacitor electrode material. Furthermore, the asymmetric supercapacitor containing a ZnCo2S4@PPy positive electrode demonstrated a high specific energy of 33.78 Wh kg−1 at 800.05 W kg−1 and relatively long cycle life (90% capacitance retention after 5000 cycles). The excellent electrochemical performance of ZnCo2S4@PPy can be attributed to the synergistic effect of its main components and unique flower-like core-shell structure. The results reveal that the ZnCo2S4@PPy core-shell nanocluster array is a promising electrode material for future energy-storage devices.