Continuously rising sea levels pose severe threats to the diversity and stability of coastal ecosystems. However, the responses of endospheric and rhizospheric arbuscular mycorrhizal (AM) fungal communities to accelerated seawater intrusion and changing vegetation types unfortunately remains unknown. Such insights will assist in revealing the structure of AM fungi across different tidal zones, enabling the development of effective measures to conserve biodiversity. Here, we investigated changes in endospheric and rhizospheric AM fungal communities associated with four types of coastal vegetation in Dafeng City, Jiangsu Province, China, in response to sea level variations by analyzing their characteristics and connections to selected environmental factors. It was found that the AM fungal communities of coastal vegetation differed significantly in their compositions, diversity, and stability (the resilience or resistance of a community). Despite the responses of endospheric and rhizospheric AM fungi to soil environmental factors, the soil electrical conductivity, cation exchange content, and inorganic carbon were identified as core elements that influenced the characteristics of AM fungal communities between different coastal vegetation species. Lastly, the major endospheric and rhizospheric species of AM fungi were important predictors that explained much of the variation in the soil environment. Consequently, the dynamics of AM fungal communities were correlated with the plant–soil system under different conditions. Apart from the coastal vegetation species, the characteristics of AM fungal communities can also be driven by high salinity and the inorganic carbon content induced by the intrusion of seawater.