To investigate the differences of fungal network structures and interaction among fungal species of in black soil region of Northeast China, Illumina MiSeq sequencing was used to reveal the fungal communities in the three long-term fertilization experimental fields. Fungal molecular ecological networks were constructed based on random matrix theory (RMT). The results demonstrated that Ascomycota, Basidiomycota and Zygomycota were the dominant phyla and Hypocreales, Pleosporales and Sordariales were the dominant order, but the relative abundance of some dominant taxa significantly varied in different locations. Fungal molecular ecological network structures in three locations showed significant difference, with more complex fungal network being observed in north location with more competitive relations among species. The fungal network in south location was more easily disturbed by environmental perturbations with less stability. Only seven shared nodes were detected among three fungal molecular ecological networks. There were large differences in connectivity of shared nodes within individual fungal network. The subnetwork of Hypocreales was gradual complex from south to north location while subnetwork of Pleosporales presented reversed trend. The key species of south, middle and north locations were Chaetomiaceae, Pleosporales and Penicillium coralligerum, respectively. Soil pH and total N content were the main soil properties simultaneously influencing three fungal networks.