The effects of calcium cyanamide on the soil fungal communities in successive tea-cuttings nursery soils were investigated based on Illumina high-throughput sequencing. The field experiment was carried out with three treatments, including control (CK), flooding (F) and calcium cyanamide (CC). The treatment with calcium cyanamide increased pH (~1 unit) and reduced the accumulation of phenols (~50%), available phosphorus (~28%) and exchangeable Al (~90%) significantly, and improved soil quality. The predominant phylum in all treatments was Ascomycota. FUNGuild revealed that the dominant trophic mode was saprotrophy in tea-cuttings nursery soil. Plant pathogens had a low abundance in the calcium cyanamide treatment. Alpha diversity analysis showed lower richness in the calcium cyanamide than the other treatments. Network analysis showed a poorly connected but highly modularized network in the calcium cyanamide treatment, with the crucial OTUs functions related to anti-pathogenicity. The results showed that calcium cyanamide should be recommended for improving long-term tea nurseries by increasing the survival rate of tea seedlings due to increasing soil pH value, reducing aluminum toxicity, decreasing the accumulation of polyphenols, diminishing pathogenic fungi and making the taxa related to anti-pathogenicity occupy a more important niche.