Quantifying physical mechanisms driving sea-level change—including global mean sea level (GMSL) and regional-to-local components (that is, sea-level budget)—is essential for reliable future projections and effective coastal management. Although previous research has attempted to resolve China’s sea-level budget from the 1950s, these studies capture short timescales and lack the long-term context necessary to fully assess modern sea-level rise in southeastern China—one of the world’s most densely populated regions with immense socioeconomic importance. Here we show that GMSL followed three distinct stages from 11,700 years before present (BP) to the modern day: (1) rapid early Holocene rise driven by the deglacial melt of land ice; (2) 4,000 years of stability from around 4200 BP to the mid-nineteenth century when regional processes dominated sea-level change; and (3) accelerating rise from the mid-nineteenth century. Our results arise from spatiotemporal hierarchical modelling of geological sea-level proxies and tide gauge data to produce site-specific sea-level budget estimates with uncertainty quantification. It is extremely likely (P ≥ 0.95) that the GMSL rise rate since 1900 (1.51 ± 0.16 mm year−1, 1σ) has exceeded any century over at least the past four millennia. Moreover, our analysis indicates that at least 94% of rapid modern urban subsidence is attributable to anthropogenic activities, with localized subsidence rates often exceeding GMSL rise. Such concurrent acceleration of global sea-level rise and rapid localized subsidence has not been observed in our Holocene geological record.