The unique components and architecture of Prussian blue analogous (PBAs) offer great potential for the construction of various functional nanostructures. Herein, we reported the preparation of a series of Mn–Fe oxides-based hybrids using Mn–Fe PBA as a template and an organic carbon source by calcination. The study focuses on revealing the interaction between the microstructure and electrochemical performance of the products obtained at different calcination temperatures. Notably, the as-derived porous Fe–Fe_0.33Mn_0.67O/C nanocubes (i.e., M600) exhibited the best rate capability and cycle life compared with other samples (∼890 mAh/g at 0.1 A/g, 626.8 mAh/g after 1000 cycles at 1.0 A/g with a 99% capacity retention). These can be attributed to the fact that the porous structure provides shorter Li⁺ diffusion path and promotes the penetration of electrolyte. Besides, the N−doped C formed by the carbonization of organic ligands can buffer the volume change and prevent the aggregation of Fe_0.33Mn_0.67O nanoparticles during the discharge/charge cycles. Moreover, the presence of metallic Fe enhances the conductivity and the electrochemical activity, which accelerates the electrochemical reactions. Therefore, reasonable design of microstructure and compositions of functional nanocomposites is the key to obtain ideal electrochemical properties.