Global changes arouse large-scale fragmentation of forests, which has a profound impact on the balance of the global carbon cycle. However, the effect and process of temperate forest fragmentation on photosynthetic carbon uptake are not clear. We used remote sensing datasets to describe the degree of forest fragmentation and clarify the relationship between fragmentation and photosynthetic carbon uptake in the temperate forests of northeastern China. The results show that forest fragmentation has high spatial heterogeneity and promotes photosynthetic carbon uptake (14% in the cold temperate zone and 10% in the middle temperate zone). Hydrothermal conditions are the dominant influencing path, explaining 60% of the variation in the cold temperate zone and 49% of the variation in the middle temperate zone. In addition, temperature is the dominant driver of the cold temperate zone, and water is the dominant driver of the middle temperate zone. Our research calls for a deeper understanding of the carbon cycle of fragmented temperate forests, and it is necessary to consider appropriate human intervention in forest management.