Electronic engineering of gallium nitride (GaN) is critical for enhancement of its electrode performance. In this work, copper (Cu) cation substituted GaN (Cu-GaN) nanowires were fabricated to understand the electronically engineered electrochemical performance for Li ion storage. Cu cation substitution was revealed at atomic level by combination of X-ray photoelectron spectroscopy (XPS), X-ray absorption fine structure (XAFS), density functional theory (DFT) simulation, and so forth. The Cu-GaN electrode delivered high capacity of 813.2 mA h g−1 at 0.1 A g−1 after 200 cycles, increased by 66% relative to the unsubstituted GaN electrode. After 2000 cycles at 10 A g−1, the reversible capacity was still maintained at 326.7 mA h g−1. The DFT calculations revealed that Cu substitution introduced the impurity electronic states and efficient interatomic electron migration, which can enhance the charge transfer efficiency and reduce the Li ion adsorption energy on the Cu-GaN electrode. The ex-situ SEM, TEM, HRTEM, and SAED analyses demonstrated the reversible intercalation Li ion storage mechanism and good structural stability. The concept of atomic-arrangement-assisted electronic engineering strategy is anticipated to open up opportunities for advanced energy storage applications.