The ordered/disordered distribution of transition metal (TM) plays a significant role in determining electrochemical properties including lattice oxygen redox, ion kinetics and structure evolution. From a novel perspective, this work demonstrates how the TM distributions influence the doping effect by means of introducing Cu element into ordered/disordered O3-Nax(NiySb1-y)O2. What’s more, the irreversible Cu migration from TM sites to Na layers upon electrochemical process is found. This migration which would deteriorate electrochemical stability only occurs in honeycomb-ordered compounds, instead of in disordered one. Theoretical calculations reveal that the TM disordered distribution promotes the formation of antibonding orbitals between Cu 3d and O 2p, thereby increasing the barrier of Cu migration to maintain well Na diffusion kinetics. Our discovery rolls out a new guidance for designing advanced cathode materials for sodium-ion batteries and speeds up the research on transition metal migration.