Here, we report that mesoporous hollow carbon spheres (HCS) can be simultaneously functionalized: (i) endohedrally by iron oxide nanoparticle and (ii) egzohedrally by manganese oxide nanorods (FexOy/MnO2/HCS). Detailed analysis reveals a high degree of graphitization of HCS structures. The mesoporous nature of carbon is further confirmed by N2 sorption/desorption and transmission electron microscopy (TEM) studies. The fabricated molecular heterostructure was tested as the anode material of a lithium-ion battery (LIB). For both metal oxides under study, their mixture stored in HCS yielded a significant increase in electrochemical performance. Its electrochemical response was compared to the HCS decorated with a single component of the respective metal oxide applied as a LIB electrode. The discharge capacity of FexOy/MnO2/HCS is 1091 mAhg−1 at 5 Ag–1, and the corresponding coulombic efficiency (CE) is as high as 98%. Therefore, the addition of MnO2 in the form of nanorods allows for boosting the nanocomposite electrochemical performance with respect to the spherical nanoparticles due to better reversible capacity and cycling performance. Thus, the structure has great potential application in the LIB field.