Soil moisture (SM) is essential for controlling terrestrial carbon uptake, as it directly provides moisture for photosynthesis, especially in arid and semiarid regions. We selected the arid and semiarid Ili River basin (IRB) of Xinjiang as the study area, and investigated the spatial and temporal characteristics and interrelationships with SM and photosynthesis from 2000 to 2018 using the ERA5 products and solar-induced chlorophyll fluorescence (SIF). SM and photosynthesis showed a decreasing trend during the study period. Compared with those in spring and autumn, the variation of summer SM and SIF was more consistent with the interannual variation. Anomaly analysis showed that negative SM anomalies were most profound in 2012–2015, 2008, and 2014. Additionally, we quantified the effect of seasonal SM deficits on photosynthesis by performing model-based experiments. The results indicated that the gross primary productivity (GPP) simulated by the P-model could capture the characteristics of photosynthesis in the IRB, which had a high correlation with SIF (R2 = 0.82, p < 0.001). In 2012–2015, 2008, and 2014, SM deficits caused more GPP reduction in the summers than in the springs or the autumns. The trends were mainly visible in the northern IRB, where GPP was below 40 % of the multi-year mean, and SM was below 23 %. GPP decreased more significantly in grassland than in the forest under the influence of SM deficit. This study reveals seasonal differences in the effects of SM deficit on photosynthesis and emphasizes that the summer SM deficit was the main factor responsible for decreases in GPP in the IRB during the study period. These findings contribute to a better understanding of the relationships between photosynthesis and environmental factors, and provide a reference for an accurate assessment of the regional carbon cycle.