Chilling is the main limiting factor for rice production in high-altitude and high-latitude regions. Many studies have reported the impacts of chilling on leaf photosynthesis and biomass accumulation, but few of them explored the response of photosynthesis to chilling at different growth stages of rice and whether the decrease of photosynthesis at each stage is caused by stomatal or non-stomatal limiting factor. In order to achieve high grain yield for rice, it is critical to understand how chilling affects leaf photosynthesis and plant growth. In this study, we conducted a two-year field experiment (in 2018 and 2019) to investigate the effects of chilling at booting, flowering, and grain filling stages on leaf photosynthesis, plant growth, and grain yield for a japonica rice cultivar (Songjing6). At each target growth stage, the treatment included four chilling temperatures (12, 15, 18, and 21 ℃, respectively) and four chilling durations (2, 4, 6, and 8 days, respectively). The results showed that rice photosynthesis gradually decreased as the chilling temperature was decreasing and the chilling duration was increasing. The net photosynthetic rate decreased the most at the booting stage, followed by the flowering stage, and the grain filling stage. Compared with the chilling treatment at 2 days, the chilling treatment at 12, 15, and 18 ℃ for 4, 6, and 8 days reduced net photosynthetic rate by 15.1–36.1 %, 18.7–27.2 %, and 15.2–17.2 % at the booting, flowering, and grain filling stages, respectively. The chilling-induced decrease in net photosynthetic rate was mainly attributed to stomatal limiting factor at the booting and flowering stages but non-stomatal limiting factor at the grain filling stage. During the chilling treatment, the available light for rice plants was reduced and the rice plants were impaired in their ability to use weak light. The decrease in photosynthesis lead to reduced leaf source capacity and crop growth rate, hence the reduced aboveground biomass and increased source and sink increment ratio, and ultimately decreased the grain yield for rice. Our results indicate that maintaining efficient photosynthetic functioning at the booting and flowering stages is the key to combat chilling stress for rice. • Chilling decreased the net photosynthetic rate of rice most at the booting stage, followed by the flowering stage and the grain filling stage. • Chilling-induced decrease in the net photosynthetic rate was mainly attributed to stomatal limiting factor at the booting and flowering stages, but non-stomatal limiting factor at the grain filling stage. • The simulation of light response curve showed chilling at the booting and flowering stages decreased photosynthetic capacity and photosynthetic effective time,while chilling mainly affects the ability of using strong light at the grain filling stage.