In this paper, it was studied that the changes of fungal community in the production of Daqu between the summer and autumn by using high-throughput sequencing technology and multivariate statistical methods. It was showed that the main fungi in the production of Daqu in summer were 14 genera as well as that were 17 genera in autumn. The main fungi in the production of Daqu in summer were all existed in Daqu produced in autumn. Pichia, Saccharomycopsis and Wickerhamomyces were the main fungi in the beginning of Daqu production in the two seasons of summer and autumn, and Pichia was the main fungus in the whole production of Daqu in autumn. Thermoascus was the main fungus in the late stage of Daqu production in summer. The fungi species in the production of Daqu in autumn were more than that in summer, but the distribution of fungi in the production of Daqu in summer was more uniform than that in autumn. The Daqu production can be divided into two stages whose dividing lines were respectively 8 d and 12 d in the summer and autumn. It was more easily affected by external conditions when Daqu produced in autumn, especially in the early stage of production.