The electronic and local atomic structural characterization of a promising cathode material, LiFe0.4Mn0.6PO4, for a lithium rechargeable battery was performed by in situ X-ray absorption fine structure (XAFS) on both Mn and Fe K-edges. Upon delithiation, the X-ray absorption near edge structure (XANES) spectra analysis showed that the Fe2+/Fe3+ electrochemical reaction was two times faster than that of Mn2+/Mn3+. The Fe and Mn K-edge extended X-ray absorption fine structure (EXAFS) spectra were effectively altered with different spectral behaviors for the local atomic structure near Fe and Mn during delithiation. Alternatively, the EXAFS spectra of LiFePO4 changed significantly and those of LiMnPO4 were constant through all delithiations for the corresponding reference materials of LiFePO4 and LiMnPO4. The present study with XAFS characterization demonstrates that initially delithiated Fe-rich domains at 3.5V can promote more effective local structural change of the neighboring Mn-rich domains during the next second plateau at 4.1V, which can ease delithiation in the Mn-rich domains through more flexible reaction of the local structure in the Mn octahedra.