This study aims to understand the influence of chlorophyll fluorescence parameters on the yield of winter wheat in some areas of China. Nitrogen (N) application is believed to improve photosynthesis in flag leaf, which ultimately increases the final yield. The experiment was conducted in the wheat experimental base of Shanxi Agricultural University in Taigu, Shanxi Province, China; before sowing, four N application rates were set—N0, N120, N150, and N210 kg ha–1 of the Yunhan-20410 variety from 2019 to 2022. The results from different parameters of research showed that the organic manure partial substitution for chemical fertilizer increased post-anthesis N uptake by 16.4 and 81.4%, thus increasing the post-anthesis photosynthetic capacity and delaying leaf senescence. N150 treatment can improve dry matter (DM) accumulation, thus promoting the increase of the yield. The maximum net photosynthesis PN value of the booting stage and flowering stage indicated that nitrogen application could significantly improve the photosynthetic rate of wheat leaves, among which medium nitrogen treatment had the most significant promoting effect. The single-photon avalanche diode (SPAD) value of the leaf of wheat in each treatment increased rapidly in a small range from the jointing stage to the booting stage, respectively. The grain yield under N fertilizer partial substitution for N fertilizer treatment increased by 23%. According to the different significance test, the effects of nitrogen application rate on net photosynthesis PN of winter wheat were extremely significant at all growth stages, indicating that changing the population distribution mode and nitrogen level could effectively improve leaf photosynthetic performance and that N150 level was the best.