Porous NiCo2O4 hetero-structure arrays on nickel foam are prepared by a facile hydrothermal method. The morphology of the arrays changes with the growth time. After hydrothermal synthesis for 8 h in combination with annealing treatment, the NiCo2O4 array presents a nanoflake–nanowire hetero-structure. The porous NiCo2O4 hetero-structure array exhibits the excellent pseudocapacitive properties in 2 M KOH, with a high capacitance of 891 F g−1 at 1 A g−1 and 619 F g−1 at 40 A g−1 before activation as well as excellent cycling stability. The specific capacitance can achieve a maximum of 1089 F g−1 at a current density of 2 A g−1, which can still retain 1058 F g−1 (97.2% retention) after 8000 cycles. The enhanced pseudocapacitive performances are mainly attributed to its unique hetero-structure which provides fast ion and electron transfer, large reaction surface area and good strain accommodation.