The medium-high temperature Daqu (ZGW) and medium temperature Daqu(ZW)are mainly used for fermentation starter for strong flavor Baijiu. In the early days, ZW was used in the production of strong flavor Baijiu. At present, most of the production of strong flavor Baijiu has turned to ZGW. However, due to the lack of in-depth understanding of the differences in flavor and mechanism of strong flavor Baijiu brewed by 2 types of Daqu, choosing ZGW or ZW has become an urgent problem for the industry. In order to regulate and control the fermentation process to obtain better quality strong flavor Baijiu, the physicochemical indexes, enzyme activity indexes and microbial community structure of 2 types of Daqu were analyzed, and the influence path and function of different microorganisms on the flavor formation of strong flavor Baijiu were deeply explored. The results showed that acidity and protease activity in ZGW were significantly higher than ZW samples(P<0.05), whereas saccharification power, liquefaction power and fermentation power in ZW were significantly higher than ZGW(P<0.05), and there were no significant differences in water, starch and reducing sugar content between the 2 types of Daqu. 20 Dominant fungal species and 20 dominant bacterial species were detected in 2 types of Daqu. According to the identification of fungal species, the main dominant fungal species of ZGW were Thermoascus aurantiacus (24.64%), Dipodascus geotrichum (13.39%), Wickerhamomyces anomalus (8.04%). The main dominant fungal species of ZW were Candida tropicalis (40.00%), Kodamaea ohmeri (12.80%), Trichosporon coremiiforme (10.98%). For bacterial species, the main dominant bacterial species of ZGW were Acinetobacter johnsonii XBB1 (32.49%), Lactobacillus sakie (16.80%), Pseudomonas putida (10.68%). The main dominant bacterial species of ZW were Lactobacillus sakie (39.32%), Acinetobacter johnsonii XBB1 (18.45%), Enterococcus faecium (13.00%). Moreover, 23 differential species were found in 2 types of Daqu,including 14 species of fungi and 9 species of bacteria. According to microbial function prediction, there were abundant enzymes about carbon and nitrogen metabolism in 2 types of Daqu. The abundance of saccharify and fermentation enzymes in ZW was higher than ZGW, indicating the potential ethanol production ability of ZW was stronger than ZGW. The abundance of enzymes related to acid production and nitrogen metabolism in ZGW was higher than ZW, indicating the potential ability of acid production and nitrogen flavor compounds in ZGW was stronger than that in ZW. Through analysis of physicochemical parameters,enzyme activity, microbial community structure and metabolic function of 2 types of Daqu, the differences between 2 types of Daqu were further understood, to provide theoretical basis and technical guidance for strong flavor Baijiu production.