Multicomponent binary metal oxide-involved hybrid structures with unique physicochemical properties have received extensive attention due to their fascinating electrochemical performance. Herein, a flexible strategy, which involves the preparation of dual-functional heterometallic Fe2M clusters and their subsequent sintering treatment, is developed to engineer novel 3D hierarchical porous structures assembled with MFe2O4 (M = Co, Mn, Ni and Zn) nanoparticles confined within carbon outer shell (denoted as MFe2O4@C HPSs). In this intriguing construction, it can be observed that MFe2O4@C HPSs comprised of carbon coated secondary MFe2O4 nanoparticles with an interconnected carbon network. The as-prepared MFe2O4@C HPSs possess combined advantages of high capacity of MFe2O4 and high conductivity of carbon. As expected, the MFe2O4@C HPSs offer a high reversible capacity, high cycling stability and superior rate performance. The interconnected conductive carbon shells facilitates fast ion and electron transport and accommodates the mechanical strain. In addition, nanosized MFe2O4 particles, which shorten the ion-transport path and provide extra electroactive sites, also improve the reaction kinetics. Moreover, these MFe2O4@C HPSs exhibit good structural integrity during repeated charging and discharging. The research perspective and strategy reported here are highly versatile and shed new light on the synthesis of other advanced electrode for various applications.