Variations in urban surface runoff are often attributed to static infrastructure, neglecting the non-stationary hydrological responses induced by rapid urbanization and intricate micro-topography. This study introduces a Pressure–Trend–Pulse (PTP) framework to examine surface runoff dynamics in Kunming, China. By integrating continuous Soil and Water Assessment Tool (SWAT) simulations (2005–2024), Sen’s slope estimation, the Mann–Kendall test, robust residual analysis, and Self-Organizing Map (SOM) clustering, we quantify these multi-dimensional changes. The findings indicate: (1) runoff displays a structural north–south gradient, with the generation centroid migrating northward at a rate of 2.3 km per decade; (2) non-stationary positive trends (0.16 mm/year) are exclusively concentrated in northern sub-basins, which constitute 26.74% of the total area, thereby exacerbating long-term cumulative pressure; and (3) detrended residual analysis reveals high-frequency pulse volatility predominantly in the southern sink areas. Overlaying 139 historical waterlogging points confirms that trend-driven and pulse-driven risks account for 30.22% and 13.67% of urban disasters, respectively. Furthermore, approximately 22% of waterlogging occurrences fall within non-significant downstream zones, implying a potential upstream-downstream source–sink decoupling. The PTP framework highlights the necessity of differentiated resilience planning: upstream source-control and downstream adaptive buffering.