Abstract Graphene oxide flexibly supported MoO 2 porous architectures (MoO 2 /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 MoO 2 particulates growing on the GO (micrometer MoO 2 /GO), 3D honeycomb‐like nanoarchitectures (MoO 2 /GO nanohoneycomb), and layered MoO 2 /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 MoO 2 /GO architectures strongly depends on their inside structures. At the current density of 100 mA g −1 , the capacities of the micrometer MoO 2 /GO, MoO 2 /GO nanohoneycomb, and layered MoO 2 /GO remain at 901, 1127, and 967 mAh g −1 after 100 cycles. The average coulombic efficiencies of micrometer MoO 2 /GO, MoO 2 /GO nanohoneycomb, and layered MoO 2 /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 MoO 2 /GO nanohoneycomb can deliver the capacity as high as 461 mAh g −1 . The MoO 2 /GO nanohoneycomb exhibits best performance attributed to its unique nanohoneycomb structure constructed with ultrafine MoO 2 fixed on the GO flexible supports.