Here we document physiological and molecular attributes of three wheat cultivars (ZM9023, YM158 and FM1228) under low light intensity with advanced technologies, including non-standard quantitative technology and quantitative proteomics technology. We found lower dry matter accumulation of YM158 compared with ZM 9023 and FM1228 under low light intensities due to up-regulation of photosynthetic parameters electron transport rate (ETR), Y(II), Fv/Fm, Chl (a + b) of YM158 and down-regulation of Chl a/b. ETR, Y(II) and Fv/Fm significantly decreased between ZM9023 and FM1228. The ETR between PSII and PSI of YM158 increased, while light use efficiency (LUE) of ZM9023 and FM1228 decreased. We found that YM158 had greater propensity to adapt to low light compared with ZM9023, as the former was able to increase photochemical electron transfer rate, enhance photosystem activity, and increase the light energy under low light. This meant that the YM158 flag leaf has stronger regulatory mechanism under low light environment. Through proteomic analysis, we found LHC protein (LHCB1, LHCB4, LHCA2, LHCA3) for YH158 was significantly up-regulated, while the PSII subunit protein of FM1228 and ZM9023 b559 subunit protein were down-regulated. We also documented enhanced light use efficiency (LUE) due to higher light capture pigment protein complex (LHC), photosystem II (PSII), PSI and cytochrome B6F-related proteins, with dry matter accumulation being positively correlated with Fv/Fm, ETR, and ΦPS(II), and negatively correlated with initial fluorescence F0. We suggest that Fv/Fm, ETR, and ΦPS(II) could be considered in shade tolerance screening to facilitate wheat breeding.