Abstract: In order to prevent and control lotus root rot and reduce the effect of rot disease on lotus root planting, the pathogen of lotus root rot disease was isolated and purified by tissue isolation and direct picking methods based on corrupted lotus root in Anning City, Yunnan Province. The types of pathogenic fungi were determined by morphological and molecular biological methods. In this study, the inhibitory effects of six pesticides (carbendazim, chlorothalonil, procymidone·thiram, mancozeb, pyraclostrobin·mebendazim, and hymexazol) on the growth of pathogenic fungi were further compared, and the optimal concentration of the agent with the best inhibitory effect is determined. In this study, a total of 6 fungus were isolated and purified from the diseased lotus root tissue, and one of them (Fusarium graminearum) could cause lotus root corruption. Among the six pesticides, chlorothalonil had the best inhibitory effect, with an inhibition rate of 56.49%, and chlorothalonil with 600-fold dilution could completely inhibit the sporulation of Fusarium graminearum. This study revealed the pathogen types of lotus root rot disease and put forward solutions, which can provide scientific guidance for the prevention and control of lotus root rot disease in Anning City.