Lilium davidii var. unicolor cotton is a famous edible lily with large-scale cultivation in China. To determine the cause of leaf yellowing in L. davidii var. unicolor, the photosynthetic characteristics and leaf structure of plants at different yellowing levels were studied. The results revealed that the chlorophyll content in the leaves of L. davidii var. unicolor decreased significantly as the degree of yellowing increased. Variation in the content of chlorophyll precursors revealed that in yellow-leafed plants, chlorophyll synthesis was impeded at the stage when coprogen is converted into Proto IX. Compared with those of normal plants, the thicknesses of the leaves, upper epidermis, palisade tissue, and spongy tissue of yellow-leafed plants were significantly lower. Distinct plasmolysis was observed in mesophyll cells. The cytomembrane and tonoplast were damaged. The number of chloroplasts and starch grains in the mesophyll cells of yellow-leafed plants decreased. The volume of chloroplasts also decreased, and structural damage occurred. Granum lamella failed to stack into granum, which led to a decrease in or disappearance of granum thylakoid. The variation in chloroplast structure and the reduction in chlorophyll content led to a further decrease in photosynthesis in yellow-leafed L. davidii var. unicolor plants. The photosynthetic parameters [net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr)] and chlorophyll fluorescence parameters [maximum quantum efficiency of photosystem II (PSII) (Fv/Fm), photochemical quantum yield of PSII [Y(II)], and electron transport rate (ETR)] decreased significantly. The Fv/Fm, Y(II), ETR, and photochemical chemical quenching were significantly positively correlated with Pn, Gs, and Tr, but highly negatively correlated with intercellular CO2 concentration (Ci) and vapor pressure saturation deficit (VPD). The results of this study provide important information for further studies of the response mechanism of plants to leaf yellowing. In addition, this study provides a theoretical basis for the prevention and recovery of yellow-leafed plants, which are important for increasing the yield and quality of L. davidii var. unicolor bulbs.