This study investigated the effects of combining Phragmites australis-based biochar, prepared at 400 °C, with various types of phosphate fertilizers—soluble, insoluble, and organic—on the content and transformation of phosphorus fractions in saline-alkali soil. Additionally, we explored microbiological mechanisms driving these transformations. The results showed that this combination significantly increased the concentrations of dicalcium phosphate (Ca2P), octacalcium phosphate (Ca8P), aluminum phosphate (AlP), moderately labile organic phosphorus (MLOP), and resistant organic phosphorus (MROP) in soil. Conversely, the levels of hydroxyapatite (Ca10P) and highly resistant organic phosphorus (HROP) decreased. The increase in labile organic phosphorus (LOP) content or decrease in iron phosphate (FeP) was found to effectively enhance the availability of Olsen phosphorus (Olsen-P) in soil. Furthermore, the study revealed that biochar mixed with organic phosphate fertilizers increased the activity of soil acid phosphatase (ACP) and neutral phosphatase (NEP), while reducing alkaline phosphatase (ALP) activity. In contrast, biochar combined with soluble and insoluble phosphate fertilizers decreased the activity of ACP (22.59 % and 28.57 %, respectively) and NEP (62.50 % and 11.11 %, respectively), with the combination with insoluble fertilizers also reducing ALP activity by 55.84 %, whereas the soluble combination increased it by 190.34 %. Additionally, the co-application of biochar and phosphate fertilizers altered the composition and abundance of the gene phoD-harboring microbial community, enhancing the abundance of Proteobacteria and reducing that of Actinobacteria. Correlation analysis between phoD-functional microbial species and various phosphorus fractions showed that Rhodopseudomonas was significantly associated with several phosphorus components, exhibiting a positive correlation with Ca2P, Ca8P, AlP, LOP, MLOP, and MROP, but a negative relationship with Ca10P. These findings suggest that the combined application of biochar and phosphate fertilizers could change the abundance of Rhodopseudomonas, potentially influencing phosphorus cycling in the soil. This research provides a strong scientific foundation for the efficient combined use of biochar and phosphate fertilizers in managing saline-alkali soil.