Coastal cities increasingly face compound flooding risks due to sea-level rise and intensifying storms. This study systematically evaluates the synergistic regulation of coastal hydrodynamics by mangrove vegetation and intertidal topography as a nature-based solution (NbS) for coastal defense. Based on the Delft3D Flexible Mesh (FM) system, we simulate tidal and storm surge scenarios in two contrasting shorelines in Shenzhen, China, the naturally evolved Xiwan Mangrove Park and the engineered Bao'an Airport coastline. Results show that intertidal topography plays a dominant role in attenuating flow velocity, while mangrove vegetation becomes the primary factor in reducing peak water levels during extreme events. A functional shift in mitigation zones occurs, from mid and low tidal flats under tidal conditions to high flats during storm surges, driven by increased inundation and canopy engagement. Additionally, a clear design threshold of 600 m planting width is identified, beyond which additional vegetation provides diminishing returns due to the complete submergence of mangrove vegetation. These findings underscore the complementary roles of topography and vegetation and offer actionable guidance for optimizing NbS strategies in site-specific, climate-adaptive coastal management.