The influences of different fertilizer treatments on spore community structure and diversity of arbuscular mycorrhizal (AM) fungi (AMF) were investigated in a long-term fertilization experiment with seven treatments: organic manure (OM), half organic manure N plus half fertilizer N (1/2 OMN), fertilizer NPK, fertilizer NP, fertilizer NK, fertilizer PK, and the control (without fertilization). Fertilization generally increased the nutrient contained in the fertilizer and treatments with NPK and 1/2 OMN produced the highest crop yields. Thirty-five species of AMF within 6 genera, including 8 previously undescribed species, were recovered. Similarly in all seven treatments, the most abundant genus was Glomus, and followed by Acaulospora. All the fertilization treatments changed AM species composition, and NK treatment had the slightest influence. Fertilization with fertilizers NP, PK and NPK markedly increased AM fungal spore density, while 1/2 OMN, OM and NK treatments showed no significant influences. All the fertilizer treatments, especially OM, significantly decreased species richness and species diversity (Shannon-Weiner index). There were no significant correlations between AM fungal parameters (spore density, species richness and species diversity) and soil properties. The findings indicate that long-term fertilization all can change AM fungal community structure and decrease species diversity, while balanced fertilization with NPK or 1/2 OMN is the most suitable fertilization regime if taking both crop yields and AM species diversity into account.