Wheat yellow-green mutant Jimai5265yg has a more efficient photosynthetic system and higher productivity than its wild type under N-deficient conditions. To understand the relationship between photosynthetic properties and the grain yield, we conducted a field experiment under different N application levels. Compared to wild type, the Jimai5265yg flag leaves had higher mesophyll conductance, photosynthetic N-use efficiency, and photorespiration in the field without N application. Chlorophyll a fluorescence analysis showed that PSII was more sensitive to photoinhibition due to lower nonphotochemical quenching (NPQ) and higher nonregulated heat dissipation. In N-deficient condition, the PSI acceptor side of Jimai5265yg was less reduced. We proposed that the photoinhibited PSII protected PSI from over-reduction through downregulation of electron transport. PCA analysis also indicated that PSI photoprotection and electron transport regulation were closely associated with grain yield. Our results suggested that the photoprotection mechanism of PSI independent of NPQ was critical for crop productivity.