Extreme meteorological events and rapid urbanization have led to serious urban flooding problems. Characterizing spatial variations in flooding susceptibility and elucidating its driving factors are essential for preventing damages from urban pluvial flooding. However, conventional methods, limited by spatial heterogeneity and the intricate mechanisms of urban flooding, frequently demonstrated a deficiency in precision when assessing flooding susceptibility in dense urban areas. Therefore, this study proposed a novel framework for an integrated assessment of urban flood susceptibility, based on a comprehensive cascade modeling chain consisting of XGBoost, SHapley Additive exPlanations (SHAP), and Partial Dependence Plots (PDP) in combination with K-means. It aimed to recognize the specific influence of urban morphology and the spatial patterns of flooding risk agglomeration under different rainfall scenarios in high-density urban areas. The XGBoost model demonstrated enhanced accuracy and robustness relative to other three benchmark models: RF, SVR, and BPDNN. This superiority was effectively validated during both training and independent testing in Shenzhen. The results indicated that urban 3D morphology characteristics were the dominant factors for waterlogging magnitude, which occupied 46.02 % of relative contribution. Through PDP analysis, multi-staged trends highlighted critical thresholds and interactions between significant indicators like building congestion degree (BCD) and floor area ratio (FAR). Specifically, optimal intervals like BCD between 0 and 0.075 coupled with FAR values between 0.5 and 1 have the potential to substantially mitigate flooding risks. These findings emphasize the need for strategic building configuration within urban planning frameworks. In terms of the spatial-temporal assessment, a significant aggregation effect of high-risk areas that prone to prolonged duration or high-intensity rainfall scenarios emerged in the old urban districts. The approach in the present study provides quantitative insights into waterlogging adaptation strategies for sustainable urban planning and design.