[Background] Microorganisms are main agents to remove pollutants in activated sludge (AS) in wastewater treatment plants (WWTPs), among them, fungi should be paid attention to as they play important roles in removing toxic compounds and improving biological transformation, etc. [Objective] The major research will be focus on to characterize and compare the diversity, composition of fungal communities in WWTPs located in north and south China, determine the influence factors of fungal community structure. [Methods] Ninety AS samples from 23 WWTPs in north China and 121 AS samples from 37 WWTPs in south China were collected, respectively. After DNA extraction and amplification, high-throughput sequencing of ITS gene was carried out using Illumina MiSeq platform. Data were processed by a variety of quantitative ecological analysis methods. [Results] Fungal community structures in AS system between north and south China were significantly different. Diversity of fungal community in south China was higher than that of north China. The dominant classes and genera in fungal community were Sordariomycetes and Glomeromycetes classes, and Ophiocordycep and Alternaria genera in south China. While they were Tremellomycetes and Saccharomycetes classes, and Trichosporon and Saccharomyces genera in north China. Members of the classes Tremellomycetes and Sodariomycetes are opportunistic pathogens, which may be potential threats to downstream organisms or human health. Abnormal growth of members in Trichosporon genus will cause sludge bulking and affect the stable operation of WWTPs. Latitude, annual average air temperature, concentration of NH4+ and the total nitrogen in influent were identified as the important factors that influence fungal community structure in WWTPs. [Conclusion] Fungal communities between north and south China were significantly different in diversity and composition as a results of geographic factors, climate factors and concentration of pollutants in influent. Accordingly, toward the efficient and stable operation of the treatment plants, it is necessary to regulate the different important communities in south and north China. Furthermore, we should pay close attention to the opportunistic pathogenic fungi and some agents that easily cause sludge bulking. Establishment of population-oriented optimal control system is necessary to control the risks.