Polypyrrole nanospheres were embedded in graphene layers (rGCP) to successfully form three-dimensional hierarchical cross-linking structure through simple hydrothermal method. The structure of rGCP composite mainly resulted from the synergistic effect of cetyltrimethyl ammonium bromide and crumpled graphene layers, which was beneficial for achieving large surface area, short ion diffusion pathway, excellent rate performance and cycling stability. As a result, the hybrid rGCP composite exhibited excellent electrochemical performance with a specific capacitance of almost 400Fg−1 at the scan rate of 1mVs−1. Furthermore, even at the high current density of 10Ag−1, it still retained the capacitance of 243.2Fg−1, and excellent cycling stability (91.8% capacitance retention even after 5000 cycles). The as-prepared hierarchical hybrid composite has promising potential in electrochemical energy storage.