Ecosystem carbon sink play a crucial role in mitigating global climate change. Over the past two decades, the Yangtze River Delta (YRD) region has experienced rapid urbanization, significantly impacting its ecosystem carbon sink function. Using the Carnegie-Ames-Stanford Approach (CASA) model and soil respiration model, this study quantitatively assessed the total ecosystem carbon sink in the YRD region from 2000 to 2020, employing global Moran’s I, hotspot analysis, standard deviational ellipse, and Structural Equation Modeling (SEM) to analyze its spatiotemporal evolution and driving factors. The results revealed three key findings: (1) The total carbon sink in the YRD region increased from 70 million tons to 104 million tons between 2000 and 2020, with high-value areas primarily distributed in the mountainous and hilly regions of the southern and southwestern parts, while low-value areas concentrated in the eastern region, centered around Shanghai and its surrounding cities. (2) During this period, 68.45% of the region experienced enhanced carbon sink function, while 15.67% showed weakening, with the center of gravity shifting 24.4 km northwest. (3) The SEM model effectively explained the complex mechanisms influencing carbon sink function, identifying the normalized difference vegetation index (NDVI), proportion of forest land (PF), and proportion of built-up land (PBL) as key mediating variables. This study reveals the spatiotemporal evolution characteristics and complex influencing mechanisms of ecosystem carbon sink function in rapidly urbanizing areas, emphasizing the importance of strengthening ecological restoration and management. The findings provide valuable reference for balancing ecological conservation and economic development in the YRD region and other rapidly urbanizing areas globally.