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Coastal vegetation not only mitigates the damage inflicted by marine disasters on coastal area, but also plays an important role in the global carbon cycle (i.e. blue carbon). Nevertheless, detailed records of both long-term changes in coastal vegetation composition and diversity, coupled with climate change and river evolution, remain sparse. To explore vegetation dynamics and their influencing factors on the coastal area of the Bohai Sea (BS) during the Holocene, in this study, we present high-resolution pollen and grain size data obtained from a sediment core of the BS. The results reveal that two rapid and abrupt changes in salt marsh vegetation are linked with the river-system changes. Within each event, a recurring pattern – starting with a decline in Cyperaceae, followed by an increase in Artemisia and Chenopodiaceae – suggests a successional process that is determined by the close relationship between Yellow River (YR) channel shifts and the wetland community dynamics. The phreatophyte Cyperaceae at the base of each sequence indicate lower saline conditions. Unchannelized river flow characterized the onset of the YR channel shift, caused a huge river-derived sediment accumulation in the floodplain, and destroyed the sedges in the coastal depression. Along with the formation of a new channel, lateral migration of the lower channel stopped, and a new intertidal mudflat was formed. Pioneer species (Chenopodiaceae, Artemisia) were the first to colonize the bare zones of the lower and middle marsh areas. In addition, the pollen results revealed that the vegetation in the Shandong Peninsula was dominated by broadleaved trees during the early Holocene (8500–6500 a BP) and by conifers and broadleaved forests in the middle Holocene (6500–3500 a BP), which was followed by an expansion of broadleaved trees (3500–1000 a BP). After 1000 a BP, human impacts are recognized as a sudden decrease in Quercus and a marked increase in secondary vegetation Pinus. The pollen-based temperature index indicated that a warmer early and late Holocene and colder middle Holocene were consistent with previously reported temperature records for North and Northwest China. The main driving factors of temperature variation in this region are insolation, greenhouse gases and the El Niño-Southern Oscillation.