We have investigated the structure and magneto-transport properties of Co2Mn(Ge0.75Ga0.25) (CMGG) Heusler alloy thin films with near-stoichiometric and Mn-rich compositions in order to understand the effect of Co-Mn anti-sites on bulk spin polarization. Anomalous x-ray diffraction measurements using synchrotron radiated x-rays confirmed that CoMn anti-sites easily form in the near-stoichiometric CMGG compound at annealing temperature higher than 400 °C, while it can be suppressed in Mn-rich CMGG films. Accordingly, large enhancement in negative anisotropic magnetoresistance of CMGG films and giant magnetoresistance (GMR) in current-perpendicular-to-plane (CPP) pseudo spin valves were observed in the Mn-rich composition. A large resistance-area product change (ΔRA) of 12.8 mΩ μm2 was demonstrated in the CPP-GMR pseudo spin valves using the Mn-rich CMGG layers after annealing at 600 °C. It is almost twice of the maximum output observed in the CPP-GMR pseudo spin valves using the near-stoichiometric CMGG. These indicate that the spin polarization of CMGG is enhanced in the Mn-rich composition through suppressing the formation of CoMn-antisites in CMGG films, being consistent with first-principle calculation results.