Heteroatom doped graphene-based materials have been illustrated to be a superior approach to improve the performance of electrode materials for supercapacitors. In this work, the graphene oxide (GO) was prepared by a modified Hummers’ method employing expanded graphite as precursor, and further etched by hydrothermal method to obtain holey graphene oxide (denoted as HHGO). The resulting HHGO was utilized to synthesize a novel nitrogen(N), sulfur(S) and phosphorus (P) tri-doped holey GO (N, S, P-HHGO) material by a hydrothermal approach utilizing ammonium dihydrogen phosphate and L-cysteine as N, S and P sources and used as supercapacitor electrode materials for the first time. The electrochemical results reveal that the N, S, P-HHGO delivers a high gravimetric capacitance of 295 F g−1 at 1 A g−1 in 2 M KOH aqueous electrolyte, outstanding rate capability with 71.2% of capacity retention rate from 1 to 20 A g−1 and excellent cycling stability with 93.5% of initial capacity retention at 3 A g−1 above 10000 cycles. The outstanding electrochemical properties of N, S, P-HHGO can be attributed to a superior pore-size distribution and the introduction of N, S and P heteroatoms, and shows great potential application in supercapacitors as well as other energy storage devices.