Urban flooding presents acute challenges in heritage cities, where dense populations and valuable cultural assets coexist. While Nature-Based Solutions (NbSs) have been widely studied, their implementation in heritage cities remains underexplored due to spatial constraints and cultural sensitivities. This study develops a quantitative evaluative framework integrating the Spatial Multi-Criteria Evaluation (SMCE) and NbSs to address urban flooding in Quanzhou, a UNESCO World Heritage site. In GIS-based spatial analysis, the framework prioritizes high-risk zones by synthesizing hydrological and socio-economic factors. The analysis reveals that the Surface Runoff Coefficient (SRC) contributes 30% to urban flooding exposure, with high building congestion and elevated PM2.5 levels exacerbating risks by 17% and 16.8%, respectively. Vulnerability mapping underscores the critical role of cultural heritage, accounting for 71.1% of the vulnerability index, and highlights priority townships such as Linjiang, Kaiyuan, and Lizhong, with integrated exposure and vulnerability rates of 11.8%, 10.3%, and 9.5%, respectively. This study proposes four NbS models tailored to heritage urban landscapes, with Solution I—direct surface infiltration—identified as the most applicable, covering 170.9 ha, followed by Solution II—subterranean stormwater infiltration—at 52.3 ha. Despite limited spatial feasibility (1.3–33.5% of township areas), the framework demonstrates significant potential for integrating NbSs with existing grey infrastructure, contributing to flood risk mitigation and broader sustainability goals. The findings provide actionable insights for urban planners and policymakers, offering a replicable methodology for the deployment of NbSs in heritage-rich urban contexts worldwide. By bridging flood risk management with cultural preservation, this work advances the discourse on resilient and sustainable urban planning.