The partially substitution of chemical fertilizers with organic materials can improve soil phosphorus (P) availability; however, the response of aggregate-associated P species and the microbial community remains unclear. We investigated P speciation transformation and the related microbial community of aggregates in a 10-year field trial containing chemical fertilizer (CC), 50 % chemical N replaced by pig manure, corn straw, and manure combined with straw. Compared to CC, the organic substitute pattern increased soil aggregate stability indices, which were positively correlated with labile and moderately labile P. The organic substitution pattern improved labile and moderately labile P in > 2 mm large macroaggregates (LM) and 0.25–2 mm macroaggregates (MA), and decreased labile P in 0.053–0.25 mm microaggregates (MI) and < 0.053 mm silt + clay (SC). CaHPO4 and MgHPO4 of labile P were the primary components in MA, while Ca(H2PO4)2 was the primary component in MI. Straw addition enhanced the relative abundance of P-solubilizing microorganisms, primarily Bacillus, in different aggregates. The labile P content was higher, and the microbial network displayed higher complexity and connectivity in MI than in aggregates of other sizes. pH was the most critical factor influencing the distribution of P species in the LM. Organic carbon and aggregate stability index were the primary factors in MA, whereas phosphatase activity was the primary factor in MI and SC. Overall, the organic substitution pattern improved aggregate stability and labile P content in LM and MA and reduced labile P in MI and SC, thereby promoting P retention. These insights advance our understanding the effects of organic fertilization on P transformation in soil aggregates, with implications for developing eco-friendly P management strategies.