Metal oxides are a promising candidate for lithium-ion battery (LIB) anodes due to their high theoretical capacity and long cycle life but also face inherent poor conductivity and volume variation, making them difficult to promote the application. The cation substitution strategy is an important means to facilitate improved rate and cycling performance. However, the effect of cation substitution on electrochemical activity is multivariate and complex, and a comprehensive and systematic analysis is essential for understanding the relationship between components and properties. Herein, the aliovalent heterogeneous Cr-substituted MnO was used as a model to systematically investigate the effects of Cr substitution on the crystal structure, electron distribution, defect construction, and electrochemical reaction processes. Theoretical calculations and experimental results reveal that Cr substitution can effectively modulate the electronic structure, build a built-in electric field, generate cationic defects, and catalyze the electrochemical reaction process, thereby improving the electrode kinetics and electrochemical activity of active materials. When the optimized Mn 0.94 Cr 0.06 O was used as the anode for LIBs, a reversible capacity of 1547.3 mAh g −1 was obtained after 450 cycles at a current density of 1 C (1 C = 756 mA g −1 for half-cells), and a reversible capacity of up to 1126.2 mAh g −1 could be maintained even after 700 cycles at a current density of 2 C. The assembled Mn 0.94 Cr 0.06 O//LiCoO 2 full cell further confirms the scalability of the heterogeneous atom substitution strategy.