Soil arbuscular mycorrhizal (AM) fungi were monitored in a 4-year experiment of nitrogen (N) and phosphorus (P) fertilization in three growing seasons (April, August, and November) under two successional stages (young and mature) in a subtropical forest of China. AM fungal extra-radical hyphal density was significantly affected by fertilization, season, and interactions between fertilization and season and between forest stage and season, but not by forest stage. The spore density of AM fungi was significantly affected by forest stage and season, but not by fertilization. Totally, 160 operational taxonomic units (OTUs) of AM fungi have been identified at a 97% sequence similarity level using Illumina MiSeq sequencing of the V4 region of the 18S rDNA. AM fungal Shannon diversity index, but not OTU richness, showed a positive response to P fertilization. The community composition of AM fungi was significantly influenced by P fertilization, but not by N fertilization, season, and forest stage. Phosphorus fertilization exhibited a negative impact on the relative abundance of the dominant Glomeraceae. This finding highlights that P availability has a strong effect on the community of AM fungi in the subtropical forest ecosystem.