Abstract: Cucumber wilt is a soil-borne disease that retards cucumber production. Intercropping can be used to reduce the prevalence of plant soil-borne diseases, and celery is widely used in intercropping because of its allelopathic property. This study was carried out to explore the effect of cucumber and celery intercropping on cucumber fusarium wilt and soil fungal diversity. Soils from celery monoculture, cucumber monoculture, and cucumber and celery intercropping were analyzed for fungal ITS diversity. The amount of OUT and the Alpha diversity of soil fungi were reduced with the intercropping. Observed species index, Shannon index, Chao1 index, and Simpson index showed reducing for the intercropping though change was not significant. Five fungal phyla were identified, among which Ascomycota, Zygomycota, and Basidiomycota were the primary ones, accounting for up to 95.50% of the total phyla with the intercropping. Cucumber and celery intercropping and cucumber monoculture appeared to be in the same cluster of phyla, clearly distinct from celery monoculture. There were 329 fungal genera that were identified, and half of their abundance was accounted for by 12 genera, specifically 50.72%, 50.47%, and 47.17% for cucumber and celery intercropping, cucumber monoculture, and celery monoculture, respectively. The genus cluster distribution was consistent with the phylum distribution. Cucumber and celery intercropping altered the structure and composition of the soil fungal community, specifically enriching fungal diversity. The information provided an insight into the use of biological means to control soil-borne diseases encountered in cucumber production.