The Yangtze River Delta (YRD) region, located inside the Yangtze River Basin, functions as a vital ecological and economic area in China, with its natural environment directly impacting human existence. This study seeks to elucidate the spatial and temporal evolution of rural resilience in the Yangtze River Delta region and its underlying mechanisms by establishing a comprehensive assessment framework for rural resilience, thereby offering a scientific foundation and policy guidance for the region’s sustainable development. The research first established the DPSIR (driving force–pressure–state–impact–response) assessment index system. Subsequently, the entropy weighting method and TOPSIS were utilized to assess and rank the rural resilience levels in the Yangtze River Delta region (Shanghai, Jiangsu, Zhejiang, and Anhui) from 2012 to 2022. Ultimately, partial least squares structural equation modeling (PLS-SEM) was employed to examine the intrinsic logical relationships among the five dimensions of the DPSIR framework and to extract conclusions. The study effectively met the goals of SDG 7 (clean water and sanitation), SDG 8 (decent work and economic growth), and SDG 11 (sustainable cities and communities). The research indicated that (1) the resilience level in the Yangtze River Delta region initially declined, then increased, and eventually attained a condition of stabilization. Changes in the “driving force”, influenced by the “response level” and environmental “pressure”, have affected the resilience level of rural areas. There is heterogeneity in the assessment values and ranges of change among provinces, with the “impact” component exhibiting the most substantial evaluation value. The findings yield policy recommendations for the implementation of diverse regional governance, the establishment of connectivity mechanisms, the customization of strategies to address the specific deficiencies of each province, and the systematic enhancement of rural resilience.