Objectives This study investigated the effects of long-term combined application of chemical fertilizer and organic fertilizer on the diversity and composition of arbuscular mycorrhizal fungi (AMF) in lateritic red soil under sweet potato cultivation, and elucidated their contributions to sweet potato yield and nutrient uptake.

Methods The study was based on a long-term fertilization experiment established in 2007 in Putian, Fujian Province, China, under a peanut-sweet potato rotation system. In the 16th year of the experiment (2023) after sweet potato harvest, five treatments were selected: no fertilizer control (CK), chemical fertilizer alone (NPK), and chemical fertilizer combined with commercial organic manure (NPK+CM), pig manure (NPK+PM), or rice straw (NPK+RS). Topsoil samples were collected to determine soil chemical properties and AMF community composition, and sweet potato yield and nutrient uptake were determined.

Results Compared with the no-fertilizer control, long-term chemical fertilizer alone significantly increased soil organic carbon and total and available nutrient contents (except total potassium), but drastically decreased soil pH from 6.29 to 4.74, causing soil acidification. Meanwhile, AMF species richness (Chao1 index) and Faith’s phylogenetic diversity were significantly reduced, while the relative abundance of Glomus increased. Compared with chemical fertilizer alone, the combined organic fertilizers not only alleviated soil acidification but also further increased soil organic carbon and nitrogen and phosphorus levels, with pig manure showing the best effect, raising soil pH back to 6.12. In addition, combined application of commercial organic manure or pig manure maintained AMF species richness (Chao1 index) and all three organic fertilizers significantly enhanced AMF Faith’s phylogenetic diversity. Relative to chemical fertilizer alone, all three organic amendments increased the abundance of Sclerocystis among the three dominant AMF groups and decreased Glomus abundance; pig manure treatment additionally significantly enriched unclassified_f_Glomeraceae. Network analysis showed that all organic fertilizers significantly altered AMF co-occurrence network structures; commercial organic manure increased network complexity, pig manure increased network connectivity, while straw treatment exhibited higher modularity. LEfSe analysis identified Glomus VTX00400 and unclassified_f_Glomeraceae ASV78 as the characteristic taxa in the commercial organic manure and pig manure treatments, respectively. Compared with chemical fertilizer alone, combined application of commercial organic manure, pig manure, and rice straw increased sweet potato yield by 11.39%, 30.70%, and 24.05%, respectively. Correlation analysis revealed that unclassified_f_Glomeraceae was significantly positively correlated with nitrogen and phosphorus uptake, while Glomus VTX00400 was significantly positively correlated with yield and phosphorus and potassium uptake. Random Forest analysis indicated that soil organic carbon was a key factor influencing sweet potato yield and nutrient uptake, and unclassified_f_Glomeraceae and Glomus VTX00400 partially explained the variation in phosphorus and potassium uptake, respectively.

Conclusions Different types of organic fertilizers exerted distinct regulatory effects on arbuscular mycorrhizal fungal (AMF) communities and their co-occurrence networks in lateritic red soil. Combined application of pig manure alleviated soil acidification, specifically enriched an unidentified genus within Glomeraceae associated with nitrogen and phosphorus uptake, and enhanced nutrient availability. Moreover, by reducing modularity and strengthening cross-module connectivity, it significantly improved overall community connectedness and synergistic symbiosis, thereby facilitating the construction of a mutualistic microbial network. Commercial organic fertilizer better maintained AMF richness and network complexity, and enriched GlomusVTX00400 linked to phosphorus and potassium acquisition. This not only intensified interspecific linkages among AMF but also preserved moderate competition and high taxonomic diversity, reflecting a strong capacity for sustaining network stability. Straw incorporation exhibited the highest modularity, promoting clear functional compartmentalization within the AMF community, minimizing redundant interactions, and mitigating disturbances to the pre-existing community structure. In summary, partial substitution of chemical fertilizer with pig manure represents a preferred strategy for simultaneously improving soil properties, optimizing AMF communities, and increasing crop yields in sweet potato systems on lateritic red soil.