Four farming patterns including double rice （DR），middle rice （MR），middle rice-rapeseed rotation （MROR）， and middle rice-pakchoi-rapeseed rotation （MRPOR） in a long-term （10 years） practices were selected to analyze the abundance and differences in community structure of fungi under different farming systems in China. The abundance and community composition of fungi in paddy soils were determined by real-time fluorescence quantitative PCR and high-throughput sequencing to analyze the differences in the abundance and community structure of fungi in soil under different farming patterns and their influencing factors. Results showed that MR， MROR and MRPOR had a significant influence on the abundance of fungi. MRPOR increased the abundance of fungi. The result of correlation analyses showed that nitrate nitrogen was significantly and positively correlated with the abundance of fungi. The crop rotation had a significant influence on the gene community structure of fungi in soil. The result of redundancy analyses showed that the content of soil water was the most significant factor affecting the community structure of fungi. In conclusion， the abundance， composition and diversity of communities of fungi in soil were different under different farming patterns of rice. The abundance of fungi was greatly affected by the content of nitrate nitrogen in soil under different farming patterns， and the community structure of fungi was mainly affected by the content of water in soil.