In this study, the effect of different NPK fertilizer rates on the colonization of arbuscular mycorrhizal fungi (AMF) in the roots of a maize hybrid under irrigated and non-irrigated conditions was investigated. The study aimed to determine the best methods for adding soil nutrients to maintain soil microbiome function and diversity. Results showed that different fertilizer treatments significantly affected AMF colonization in maize hybrid roots, especially under non-irrigated conditions. The results suggest that optimized fertilizer application could improve AMF colonization and maize growth under different water conditions. The research could provide useful information for future reference on how to maintain soil microbiome function and diversity.