Manganese-based compounds are expected to become promising candidates for lithium-ion battery anodes by virtue of their high theoretical specific capacity and low conversion potential. However, their application is hindered by their inferior electrical conductivity and drastic volume variations. In this work, a unique heterostructure composed of MnO and MnS spatially confined in pyrolytic carbon microspheres (MnO@MnS/C) was synthesized through an integrated solvothermal method, calcination, and low-temperature vulcanization technology. In this architecture, heterostructured MnO@MnS nanoparticles (∼10 nm) are uniformly embedded into the carbonaceous microsphere matrix to maintain the structural stability of the composite. Benefiting from the combination of structural and compositional features, the MnO@MnS/C enables abundance in electrochemically active sites, alleviated volumetric variation, a rich conductive network, and enhanced lithium-ion diffusion kinetics, thus yielding remarkable rate capability (1235 mAh·g-1 at 0.2 A·g-1 and 608 mAh·g-1 at 3.2 A·g-1) and exceptional cycling stability (522 mAh·g-1 after 2000 cycles at 3.0 A·g-1) as a competitive anode material for lithium-ion batteries. Density functional theory calculations unveil that the heterostructure promotes the transfer of electrons with improved conductivity and also accelerates the migration of lithium ions with reduced polarization resistance. This combined with the enhancement brought by spatial confinement endows the MnO@MnS/C with remarkable lithium storage performance.