Understanding variations in marine phytoplankton primary production (PP) is crucial for assessing the response of the marine environment to climate change and for quantifying the ocean carbon cycle. However, the spatiotemporal variability of size-fractionated PP in the South China Sea (SCS) remains ambiguous. Our study investigated the monthly, seasonal, and inter-annual variability of size-fractionated PP in the SCS using satellite observations from 2002 to 2022. There were noticeable seasonal and monthly variations in size-fractionated PP, with notably high PP values appearing during the cold season. The disparities in distribution and the distinct fluctuation patterns between size-fractionated PP suggest that total PP alone is not a comprehensive indicator of marine ecosystem health. Over the past two decades in the SCS, there were more pronounced decreases in total, pico-, and nano-PP, whereas micro-PP displayed no significant trend. The most pronounced decline occurred in the northern SCS, contrasted by increases in coastal areas. These size-fractionated PP anomalies showed strong correlations with climate change indices, highlighting the impact of environmental factors on these anomalies, such as sea surface temperature, mixed layer depth, and wind speed. Our findings emphasize the importance considering size-fractionated PP to gain a more nuanced understanding of the ocean carbon cycle and the marine ecosystem's response to climate changes.