Abstract:[Background] Mollisols in Northeast China are rich in organic matter and fertile soil, which become an important food production base in China and a sensitive area affected by climate change. Soil microorganism is sensitive to the changes of environmental factors and closely related to the soil fertility. Therefore, it is helpful to maintain the productivity of mollisols by studying the influence of environmental factors on soil microorganism. [Objective] Explore the effects of organic matter contents and climatic conditions on fungal community structure and diversity in arable mollisols, and provide important basic data and theoretical basis for agricultural sustainable development in mollisols regions under global climate change. [Methods] Long-term soil spatial transplant experiments were used in the present study and the species of fungi in mollisols, and the diversity and community structure of fungi were analyzed by Illumina Miseq sequencing. [Results] Under the two climatic conditions, there were abundant fungal species in arable mollisols with different organic matter contents. The content of soil organic matter had little effect on fungal diversity, while the climate conditions and fertilizer application largely affected the fungal diversity. The dominant fungi phyla in mollisols with five organic matter contents were Ascomycota, Basidiomycota, and Zygomycota, accounting for 92.5% of all the sequences. Under the colder climate, OTU numbers, Chao1, Shannon and Simpson indices all decreased in varying degrees; fertilization also reduced the number and diversity of fungi in arable mollisols, but the decreasing rate decreased as increase of organic matter contents. Climate conditions, organic matter contents, total nitrogen, fertilization and pH were the main factors that driving the changes of fungal community structure in arable mollisols with different organic matter contents. [Conclusion] Organic matter contents, fertilization and climate conditions changed the composition, diversity, and structure of the fungal community in arable mollisols. Climate conditions and fertilization had a greater impact on the fungal community structure of mollisols with different contents, while organic matter contents had a smaller effect on it. However, the effects of the first two factors would weaken with the increase of soil organic matter contents, which was obvious in Ascomycota.