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Photosynthesis is the fundamental basis of plant growth and development, and the improvement of photosynthetic efficiency can therefore promote increased crop yields. In this study, a comparative analysis of photosynthetic physiology and transcriptome was conducted between the high photosynthetic efficient variety BN207 and its parents BN64 and ZM16. The higher chlorophyll fluorescence, chlorophyll and carotenoid contents, and Lhcb1 protein accumulation in BN207 improved photosynthetic efficiency by promoting light energy absorption and conversion. Chloroplasts being distributed more closely to the cell membrane and the higher Rubisco enzyme activity of BN207 enhanced carbon assimilation, resulting in more carbohydrate accumulation in BN207. Transcriptome analysis revealed that there were several key genes mediating the high photosynthetic efficiency of BN207:TraesCS5D02G364100 (chlorophyllase), BGI_novel_G006617 (lycopene ?-cyclase), TraesCS4A02G034800 and TraesCS4A02G035100 (Zeaxanthin epoxidase), TraesCS6B02G122500 (light-harvesting complex Ⅱ chlorophyll a/b binding protein 1). These genes improved the photosynthetic efficiency of BN207 mainly by reducing chlorophyll degradation, promoting carotenoid synthesis, and increasing Lhcb1 protein accumulation. These findings provide important background information for the cultivation of wheat varieties with high photosynthetic efficiency.