Three problems are analyzed for the large generator-transformer unit over-excitation protection， i.e. the matching between protection operating characteristic curve and equipment's over-excitation curve， the performance of protection algorithm and the related problems about protection application. For the first two problems， the performance of several operating characteristic curves and algorithms are compared and analyzed. The analysis results show that the segmental fitting operating characteristic curve and the algorithm based on the inverse time protection basic relation between operation state and action value have better performance， the protection scheme combining the operating characteristic curve and algorithm can protect generator-transformer unit more effectively. For the third problem， the voltage， setting points and operating modes of protection should be fine tuned， to achieve both high efficiency and safe operation for the generators.