Canopy photosynthetic productivity is crucial for the formation of crop yields. Identifying limiting factors and adjustment targets for canopy photosynthesis in specific climates is important for yield increase. However, conducting relevant quantitative research remains challenging. In this study, two typical regions with distinct climatic characteristics were selected for a two-year trial of greenhouse tomatoes grown in different seasons. A three-dimensional canopy photosynthesis model was developed to quantify the factor contributions to the regional differences in accumulated canopy photosynthesis throughout the entire growing season (ACP), and to predict gains in ACP through three scenarios: leaf photosynthetic modifications (S1), plant layout adjustments (S2), and greenhouse film haze increase (S3). The results indicated that differences in ACP were mainly influenced by light environment (LE), leaf photosynthetic physiology (PP), and LE-PP interaction in spring, and canopy structure (CS), PP, LE, and LE-PP interaction in autumn. The predicted ACP enhancement showed as S1 > S2 > S3, with S3 showing a more limited effect. The light quantum efficiency under limiting light (κ_2LL) and maximum electron transport rate (J_max) were identified as key biochemical phenotypes for tomato high photosynthetic efficiency breeding in different environments. Additionally, adjusting row spacing under current planting density could further improve ACP. Our conclusions could assist researchers in deepening their understanding of canopy photosynthesis limitations under real production conditions, and provide a theoretical foundation for optimizing greenhouse tomato yield in the context of climate change.