Graphene oxide flexibly supported MoO2 porous architectures (MoO2/GO) by decomposition of the prepared ammonium molybdate/GO preforms is fabricated. Focused ion beam microscope analysis shows that the inside structures of the architectures strongly depend on the percentages of the GO used as flexible supports: micrometer scale MoO2 particulates growing on the GO (micrometer MoO2/GO), 3D honeycomb‐like nanoarchitectures (MoO2/GO nanohoneycomb), and layered MoO2/GO architectures are achieved at the percentage of GO at 4.3, 15.2, and 20.8 wt%, respectively. The lithium storage performance of the MoO2/GO architectures strongly depends on their inside structures. At the current density of 100 mA g−1, the capacities of the micrometer MoO2/GO, MoO2/GO nanohoneycomb, and layered MoO2/GO remain at 901, 1127, and 967 mAh g−1 after 100 cycles. The average coulombic efficiencies of micrometer MoO2/GO, MoO2/GO nanohoneycomb, and layered MoO2/GO electrodes are 97.6%, 99.3%, and 99.0%. Moreover, the rate performance shows even cycled at a high current density of 5000 mA g−1, the MoO2/GO nanohoneycomb can deliver the capacity as high as 461 mAh g−1. The MoO2/GO nanohoneycomb exhibits best performance attributed to its unique nanohoneycomb structure constructed with ultrafine MoO2 fixed on the GO flexible supports. MoO2/graphene oxide (GO) architectures are achieved by decomposition of the prepared ammonium molybdate/GO preforms. The nanohoneycomb‐like nanoarchitectures are achieved at the optimized ratio with high MoO2 loading 84.8 wt%. The Li‐ion storage capability is significantly improved attributed to their unique nanohoneycomb architectures constructed with ultrafine MoO2 fixed on the GO flexible supports.