With the intensification of coastal human activities, hydraulic engineering projects like tide gates have reduced runoff, leading to saltwater intrusion (SWI) events in estuaries. SWI has altered the original salinity, redox conditions, and other physicochemical parameters in the estuary, subsequently affecting the biochemical behavior of sediment phosphorus (P). This study focused on the Liao River Estuary (LRE) in northern China, and sediment samples were collected from the sandy mouth and muddy area during and after the SWI in summer. These samples represented varying degrees of SWI. Using sequential extraction experiments, in situ high-resolution HR-Peeper, DGT technology, qPCR, and high-throughput sequencing of 16s rRNA, we analyzed the changes in P forms and release potentials in sediments and characterized the phosphorus-iron (P-Fe) coupling cycle mediated by functional microorganisms. The results indicated that calcium-bound phosphorus (HCl-P) is the primary form of P in the sediments. After SWI, both total phosphorus (TP) content and bioavailable phosphorus (BAP) in the sandy mouth area decreased, while the release flux of soluble reactive phosphorus (SRP) and soluble iron (Fe²⁺) from sediments to pore water increased. In contrast, the changes in BAP and SRP in the muddy area were reversed. This indicated that after restoring the low-salinity condition, the enhanced alkaline phosphatase (ALP) activity of the sandy mouth area facilitated greater utilization of BAP, leading to increased P release to pore water. Moreover, during the SWI, DGT bioavailable P and DGT bioavailable Fe exhibited significant synchronous variation trends, suggesting that Fe reduction in sediments dominated the P reactivation. However, this synchronous trend weakened after SWI ended. Additionally, after SWI, ALP content and the abundance of phoD genes were significantly reduced in muddy areas. The community composition of phosphorus-solubilizing bacteria (PSB) and iron-reducing bacteria (FeRB) in sediments changed significantly, with the dominant species of PSB changing from Planococcus genus to Bacillus genus, which is better adapted to low salinity conditions. Salinity (Sal) and organic phosphorus content (NaOH-nrP) were identified as the main factors influencing the changes in the community structure of PSB. Overall, this study focused on the effects of SWI on the forms of P in estuarine sediments, the P-Fe coupling cycle, and the characteristics of microbial communities, providing new insights into the impact of SWI on P cycling.