Experimental synthesis of two-dimensional MoS₂-on-MXene heterostructures and phase control of MoS₂ have been demonstrated recently. Here, the electronic, electrochemical, mechanical properties, and structural morphology of MoS₂@Ti₂C and MoS₂@Ti₂CO₂ heterostructures as anode materials for lithium-ion batteries are systematically investigated by taking advantages of van der Waals corrected spin-polarized density functional theory to give atomistic insights. The results herein demonstrate that, for the MoS₂@Ti₂CO₂ heterostructure, MoS₂ polymorph drastically affects the electronic structure and lithium (Li) diffusion at the interface. Li diffusion barrier at the interface of dT-MoS₂@Ti₂CO₂ along zigzag direction (0.15 eV) is much smaller than that of H-MoS₂@Ti₂CO₂ (0.67 eV). For the MoS₂@Ti₂C heterostructure, however, the Li diffusion behavior and electronic structure are relatively insensitive to MoS₂ morphology. Especially, the MoS₂@Ti₂C heterostructures shows ultralow diffusion barrier, high charge–discharge rate, very low open-circuit voltage (0.62–0.25 V), and high mechanical flexibility. These results suggest that MoS₂@MXene heterostructures are promising anode materials for lithium-ion batteries.