Monascus is a key fungus in Hongqu rice wine brewing system， which plays an important role in the color， aroma， taste and healthy function of the rice wine. However， the number of Monascus in the brewing process is gradually decreased， and its inhibition mechanism factor is still unknown. In order to explore the growth inhibitory factors of Monascus in the process of brewing of Hongqu rice wine， PCR-DGGE and qPCR were used to track the changes of Monascus and other dominant fungi in the traditional brewing process. The possible reasons were deduced according to the change of the amount of Monascus and were verified by the corresponding systems. The results showed that the Monascus and Saccharomyces cerevisiae were the dominant bacteria in the traditional brewing process， and the amount of Monascus decreased gradually with the brewing. The validation system indicated that the growth of Monascus could not significantly inhibit by a temporary decrease in dissolved oxygen content， the physical constraint of Hongqu and the soluble substances of Hongqu. However， increased alcohol content is the key factor affecting the growth of Monascus. The relationship between the growth change of alcohol and Monascus was further verified by the traditional brewing process. At the very beginning， the alcoholic content （0 to 4%， volume fraction） had no effect on Monascus. With the increase of alcohol content， the growth of Monascus was gradually inhibited. When the alcohol content reached 17% （volume fraction）， Monascus was significantly inhibited. Therefore， this study demonstrates that the production of alcohol is the main factor inhibiting the growth of Monascus in the fermentation process.