Metal–organic framework (MOF)-derived transition metal compounds and their composites have attracted great interest for applications in energy conversion and storage. In this work, hexagonal micro-prisms of Ni-doped CoTiO3 composited with amorphous carbon (NixCTO/C) were synthesized using Ti-Co-based MOFs as precursors. The experimental results indicate the substitutional doping of Ni2+ for Co2+ in CoTiO3 (CTO), leading to improved conductivity, as further confirmed by density functional theory calculations. Thus, the carbon-free sample of Ni-doped CTO exhibits improved lithium storage properties compared to the pristine one. Furthermore, when coupled with in situ-formed carbon, the dually modified Ni0.05CTO/C micro-prisms demonstrated a significantly increased reversible capacity of 584.8 mA h g−1, excellent rate capability, and superior cycling stability at a high current density of 500 mA g−1. This enhanced electrochemical performance can be attributed to the synergistic effect of Ni doping and carbon coating.