Reliable biological sea-level indicators are essential for improving the precision of Holocene relative sea-level (RSL) reconstructions and understanding coastal responses to future sea-level rise. However, traditional microfacies-based reconstructions are often constrained by limited vertical precision in sedimentary archives, highlighting the need for quantitative biological proxies that can be incorporated into transfer-function approaches. We investigate modern vegetation zonation and pollen transport dynamics across tidal-flat transects in southern Hangzhou Bay, eastern China, to establish a pollen-based sea-level indicator system for quantitative RSL reconstruction. Results demonstrate that modern pollen assemblages encode robust tidal-elevation signals: (1) allochthonous Pinus pollen dominates unvegetated lower intertidal zones and Spartina alterniflora-sparse middle flats, exhibiting a significant inverse relationship with elevation; (2) autochthonous Chenopodiaceae and Taraxacum pollen display strong positive elevational relationships, reaching maximum abundances in upper intertidal marshes and supratidal terrestrial interfaces; and (3) Poaceae pollen shows limited indicative value because of combined airborne and hydrodynamic transport pathways, resulting in relatively homogeneous distributions across tidal zones. These modern pollen–elevation relationships provide the foundation for developing quantitative pollen-based transfer functions, enabling probabilistic estimation of paleomarsh elevation and associated uncertainties. The calibrated indicator system is subsequently applied to sediment cores from southern Hangzhou Bay and the Yangtze River Delta to generate quantitative Holocene relative sea-level reconstructions and evaluate regional coastal environmental evolution. This study demonstrates that pollen provides a robust biological proxy for improving the vertical precision of sea-level index points and offers an independent framework for high-resolution Holocene RSL reconstruction in coastal environments.