In the Min River estuarine wetlands, we investigated the changes in soil physicochemical properties, plant biomass, and soil phosphorus (P) forms in Cyperus malaccensis wetlands and bare mudflats under different salinity conditions, to assess the impact of the increased salinity on the changes in soil P forms and their regulating factors. The results showed that: (1) Across diverse salinity conditions, soil total P and various P forms consistently showed higher levels in C. malaccensis wetlands than in bare mudflats, with a notable significance under freshwater conditions. Overall, as salinity increased, soil total P and organic P contents gradually decreased, while inorganic P and NaOH-P contents initially decreased then increased, and HCl-P gradually increased. Inorganic P was identified as the primary form of soil total P in the Min River estuarine wetlands, accounting for 74%, 77%, and 83% of total P, with the proportion increasing with salinity. (2) Under varying vegetation conditions, soil total carbon (C), total nitrogen (N), and N:P ratios in C. malaccensis wetlands surpassed those in bare mudflat soils (P < 0.05). Furthermore, in different salinity conditions, soil total C, total N, and C:N ratios in freshwater sites were notably higher than in saltwater wetlands, with high salinity areas exceeding moderate (P < 0.05). (3) Plant aboveground and belowground biomass exhibited distinct trends along the salinity gradient. Aboveground biomass increased with rising salinity, while belowground biomass was more substantial in freshwater sites than in saltwater, particularly significantly higher in moderately salinity. (4) Correlation analysis indicated that changes in salinity and its associated aboveground/belowground biomass, total C, total N, and organic matter collectively regulated the variations in soil P forms and availability. The study suggests that increasing salinity in coastal estuarine wetlands alters soil organic matter content and aboveground/belowground biomass, thereby influencing the forms and transformation of soil P. This, in turn, has implications for nutrient cycling and stoichiometric balance in wetland ecosystems.