In this study, a porous manganous oxide/graphene aerogel (MnO/GA) is synthesized via a facile sol-gel method used for the anode material of lithium-ion capacitor (LIC). The crystal and morphology characterizations confirm that the MnO nanocrystal grows directly on the graphene sheets of the three-dimensional graphene aerogel (GA) matrix. In a half-cell, the MnO/GA electrode loaded with 2.9 wt% MnO exhibits high specific capacity of 630 mAh g−1 at a current density of 0.1 A g−1 after 100 cycles. The electrochemical results show that the MnO nanocrystals loaded on the GA can enlarge the average pore size and improve the specific capacity. In addition, the porous GA matrix cannot only facilitate capacitive storage of Li+ ions but also accommodate the volume variation of MnO during conversion process. The assembled LICs using the pre-lithiated MnO/GA anode and lithium iron phosphate cathode deliver high energy densities of 194 and 93 Wh·kg−1 at power densities of 300 and 3600 W kg−1, respectively. Furthermore, the LICs exhibit superior cycling stability after 1000 cycles, with high energy density of 101 Wh·kg−1 at a power density of 300 W kg−1.