Both nitrogen (N) and phosphorus (P) additions in soils can increase tree photosynthetic rate (Pn), biomass accumulation and further increase primary production of plantation. However, the improved photosynthetic ability is varied from the added nutrient types and the mechanisms are sophisticated. In this study, an iTRAQ-based quantitative proteome combined with physiological analysis of Chinese fir (Cunninghamia lanceolata) leaves was performed to determine the common and different responses on photosynthetic process to the N and P additions. The results showed that, either N or P added in soils significantly increased Pn, but N addition had more positive effects than P addition in improving photosynthetic ability. Physiologically, N addition caused more in improving photosynthetic rate than P addition, which attributes to higher leaf N and chlorophyll contents, enlarged chloroplast size and more number of thylakoids. Proteomic data revealed that the increased Pn to N and P additions may attribute to the increased abundance of proteins involved in carbon fixation and RuBP regeneration during the light-independent reactions. However, N addition increased the abundance of photosystem II related proteins and P addition increased the abundance of photosystem I related proteins. Additionally, proteomic data also gave some clues on the different metabolic processes caused by N and P additions on glycolysis and TCA cycle, which were potentially related to higher growth and developmental rates of C. lanceolata. Therefore, this study provides new insights into the different photosynthesis and metabolic processes of Chinese fir in response to N and P additions. Fertilization is an important management measure to improve timber yield and primary production of Cunninghamia lanceolata, which is the largest planted coniferous species in southeast China. Nitrogen (N) and phosphorus (P) additions into soils can improve tree photosynthesis, and further increase plantation production. However, the mechanism of N and P additions in improving photosynthesis is still unclearly. In this study, a physiological measurement combined with proteomic analysis was performed on a controlled experiment in the greenhouse. These results improve understanding of the essentially photosynthetic activity and metabolic process of C. lanceolata responding to N and P fertilization.