<p>Forest fragmentation is a key ecological process influencing the functions of forest ecosystems, particularly in the context of rapid urbanization. However, at the national scale, the regional changes of forest fragmentation and its effects on forest carbon sequestration capacity (CSC) remain unclear in urban agglomerations. Based on the established Forest Fragmentation Index (FFI), this study assessed the regional heterogeneity of forest fragmentation and systematically analyzed the nonlinear response of CSC to FFI, using a piecewise linear regression model, an XGBoost-SHAP framework, and PLS-SEM. We found that the average FFI across all urban agglomerations was 0.45, with 54.96% of the area exhibiting moderate fragmentation (FFI = 0.4 − 0.6). The average FFI in urban agglomerations was highest in subtropical monsoon climate (SMC) zones and lowest in temperate continental climate (TCC) zones. CSC showed a distinct spatial pattern of “stronger in low latitudes and coastal (eastern) regions, weaker in high latitudes and inland (western) regions”. Nationally, 34.4% of the regions exhibited CSC levels ranging from 400 to 600&#xa0;g·m⁻²·a⁻¹, with the highest mean CSC in SMC and the lowest in TCC. We identified clear FFI thresholds affecting CSC across different climate zones: 0.48 in TCC, 0.39 in temperate monsoon climate (TMC), and 0.36 in SMC. While low levels of fragmentation may have marginal positive effects, high fragmentation significantly threatens CSC. Moreover, in the TCC zone, temperature was the dominant driver, with FFI enhancing CSC primarily through positive pathways mediated by temperature and leaf area index (LAI). In contrast, in the TMC and SMC zones, evapotranspiration (ET) was the dominant factor, and FFI suppressed CSC by reducing LAI and ET. This study reveals the complex mechanisms by which forest fragmentation, coupled with multiple factors, drives CSC, providing scientific insights for urban forest management and carbon neutrality policies.</p> Graphical Abstract <p></p>