Ecological resilience (ER) describes an ecosystem’s capacity to resist, adapt to, and recover from external shocks. Enhancing ER has become a crucial issue of high-quality development in urban agglomerations. Based on the perspective of human–land relationship, this study takes the Chengdu–Chongqing urban agglomeration (CCUA) as its research subject and constructs a three-dimensional evaluation framework of “Resistance-Adaptation-Recovery” (Res-Ada-Rec), evaluates the spatial and temporal evolution characteristics of ER from 2003 to 2022, and uses a partial least squares structural equation model (PLS-SEM) to reveal the interaction mechanism of human and natural factors on ER. Results indicate that: (1) Temporally, ER in the CCUA showed a significant upward trend, with resistance, adaptation, and recovery demonstrating fluctuating evolutionary processes. (2) Spatially, ER presented a pattern of “small agglomeration and large dispersion”, with clear spatial heterogeneity observed across the three dimensions. (3) PLS-SEM analysis revealed that green innovation, institutional policies, and the natural environment had significant positive direct effects on ER, with path coefficients of 0.54, 0.53, and 0.12, respectively. Urbanization exerted a significant indirect negative effect on ER through its impact on the natural environment. These findings deepen our understanding of how green innovation, institutional policies, and urbanization influence ER, providing scientific references for urban agglomeration to achieve modernization characterized by harmonious coexistence between humans and nature.