A series of high quality zinc oxide (ZnO) nanocrystal films doped with Ge at different Ge/Zn molar ratios were synthesized by the sol-gel method, and structural and compositional changes induced by Ge doping in the ZnO films were analyzed by x-ray diffraction, x-ray photoelectron spectroscopy and cathodoluminescence spectroscopy. Heavy Ge doping in ZnO was found to effectively reduce intrinsic defects in the films and suppress free exciton emission and defect-related emissions in the visible green-red region, by the substitution of Ge at Zn sites and the formation of non-radiative deep-level traps (GeZn)+. The generation of such non-radiative traps was found to be suppressed with respect to the dopant increase, because of a reduction in carrier concentration along with a formation of stable defect complex GeZn–VZn at high doping content. The clarification of defect alterations in Ge-doped ZnO lays the foundation of quantitative evaluation of defect effects on the electrical and optical properties for improving the quality of GeZnO devices.