【Objective】This study aimed to understand the key processes that drive the changes in diversity and community assembly of arbuscular mycorrhizal (AM) fungi in greenhouse ecosystem.【Method】Soil samples were collected during different growth stages (i.e., fallow period, flowering stage, fruiting stage) of tomatoes in a greenhouse. Illumina MiSeq high-throughput pyrosequencing was performed to investigate the changes in taxonomic and phylogenetic diversity and community structure of AM fungi. The relative importance of stochastic and deterministic processes in structuring AM fungal community at different growth stages was analyzed by phylogenetic structure analysis.【Result】Results showed that both taxonomic and phylogenetic diversity of AM fungi varied significantly across different growth stages. Compared with the fallow period, OTU richness, Shannon diversity, Pielou evenness, phylogenetic diversity (PD) and mean pairwise phylogenetic distance (MPD) of AM fungi significantly decreased by 42.82% - 59.18%、43.25% - 48.31%、17.46% - 25.40%、57.14% - 67.86% and 50.00%, respectively, during the flowering and fruiting stages. In addition, the relative abundance of Glomus was promoted in the growing period, whereas the relative abundance of Claroideoglomus and Paraglomus decreased. Also the relative abundance of Archaeospora followed a unimodal pattern. Results of permutational multivariate analysis of variance (PERMANOVA) and non-metric multidimensional scaling analysis (NMDS) showed that, based on both taxonomic and phylogenetic data, the community structure of AM fungi in tomato soils during the fallow period was significantly different from that of the growing period, while the difference in community composition between the flowering and fruiting stage was not significant. According to the phylogenetic structure analysis, we found that the mean net relatedness index (NRI) across all samples was equal to zero at the fallow period, indicating phylogenetic random of AM fungal community, whereas the mean NRI was significantly greater than zero in both the flowering and the fruiting stages, indicating phylogenetic clustered. These results suggest that the primary ecological process structuring communities shifted from a stochastic process at early succession to a deterministic process at the tomato growing stage when local environmental filtering increased, which inference was also supported by the neutral community model (NCM) results. Mantel test showed that soil pH, soil nutrients (SOC, total NPK, and Olsen-P) and salt content, as well as soil temperature and humidity, significantly affected the seasonal changes of AM fungal community.【Conclusion】The highly intensive production stress in the greenhouse vegetable ecosystem promoted the transformation of the primary ecological process of AM fungal community assembly from a random process to a deterministic process, leading to a decrease in diversity and a change in community structure. Our results reveal the degradation of soil quality and the evolution of the microbiome in the process of greenhouse vegetable cultivation.