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Consecutive tomato monoculture cropping (CTM) obstacles severely restrict the development of facility tomato industry in China. However, the effect of CTM on the soil fungal community in greenhouses is still unclear. Here, we aim to identify the variation of soil chemical properties and soil fungal community associated with CTM for 1, 3, 5, 9 and 13 cycles. The results indicated that CTM led to a significant increase in soil total phosphorus (TP) and soil electrical conductivity (EC) value. CTM, though, significantly increased soil fungal community diversity, yet also led to the imbalance of soil fungal community compositions. Specifically, a beneficial soil fungus, <i>Chaetomiaceae</i>, decreased significantly at CTM13, while several soil pathogenic fungi, including <i>Fusarium</i> and <i>Cladosporium</i>, increased significantly at CTM13. A redundancy analysis (RDA) indicated that soil EC value, pH and TP had a greater impact on soil fungal community structure. Structural-equation-model (SEM) analysis indicated that, when compared with CTM3–CTM9, the decline of tomato fruit fresh weight per plant (TFFW) at CTM13 might be related to the significant increase in soil EC value, soil <i>Fusarium</i> and <i>Cladosporium</i>. Thus, appropriately decreasing soil EC and soil pathogenic fungi and enhancing soil beneficial fungi under a CTM system is crucially important for sustainable tomato production in greenhouses.