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Soil fungi played important roles in the maintenance of soil fertility and soil sustainable development. In this study, the effects of different fertilisers (i.e. bacterial fertiliser (BF), composed of organic matters and bacteria; mineral fertiliser (MF), composed of N, P and K) on soil fungi in wheat field were analysed. The results showed that the yield of winter wheat with BF was 4 788.52 kg/ha, which was significantly higher than that with term MF. Chao 1<br />and Shannon indexes and principal coordinates analysis showed that fertilisation increased the richness of soil fungi to varying degrees and changed the fungal community structure of soil compared with no fertiliser control (NF). The soil fungal community was mainly composed of Ascomycota, Basidiomycota and Mortierellomycota, with Ascomycota as the main species (62.67–65.08%). Compared with MF, the relative abundance of potential beneficial fungi Talaromyces in BF increased 4.44 times. Compared with no fertiliser control, the relative abundance of potential beneficial fungi Chrysosporium in BF increased 4.11 times. The abundance of potential soil pathogenic fungi (P &lt; 0.01), like Stachybotrys, Acrocalymma, Achroiostachys, Arachnomyces and Setophoma, significantly decreased in BF treatment, which was beneficial to the maintenance of crop health and the sustainable development of the environment. Moreover, the network analysis showed that the interspecific relationship of soil fungi in BF was more intimate than MF and NF and fungi were inclined to adopt cooperative manner to adapt ecological niches in BF treatment. The improvement of wheat yield might be due to the optimisation of soil fungal community structure by applying BF, which strengthened the transformation of nutrients in soil, increased some biocontrol microorganism, and reduced the crop disease. The results explain the improvement of wheat yield by BF to a certain extent, and provided theoretical basis for high-yield cultivation of wheat.