Purpose Fe-modified biochar could promote soil organic phosphorus (P-o) mineralization and phosphorus (P) bioavailability; however, the role of biochar and Fe-modified biochar in driving the mineralization of P-o by phoD-harboring bacteria in soil aggregates was less known, especially in saline-alkali paddy soil. Methods A 5-year paddy field experiment was conducted in Yellow River Delta, in which four fertilization treatments were designed: no fertilization (Control), inorganic fertilizer (NPK), NPK +biochar (BC), and NPK +Fe-modified biochar (FeBC). Results Compared with NPK treatment, the proportion of macroaggregates in BC and FeBC treatments was significantly increased by 10.42% and 24.67%, respectively. And the mean weight diameter was also increased under biochar treatments. Redundancy analysis (RDA) indicated that oxalate-extractable Fe was a main factor in the stability of soil aggregates, which was significantly increased in FeBC treatment. Meanwhile, the relative abundance of phoD-harboring bacteria was increased in both BC and FeBC treatments, which was driven by the content of soil organic carbon. And the diversity of phoD-harboring bacteria was positively correlated with P-o mineralization. Meanwhile, compared with NPK treatment, the activity of alkaline phosphatase in macroaggregate was increased by 39.1% in FeBC treatments, which also promoted the mineralization of soil P-o. Conclusions Therefore, biochar addition, especially Fe-modified biochar combined with mineral fertilization, was a better strategy in improving soil aggregate structure and promoting P-o mineralization in saline-alkaline paddy soil.