Abstract: The aims are to screen out the chemicals that can effectively control cotton wilt, reduce blindness of farmers’medication, improve control level of the disease, and enhance economic benefits of cotton in Xinjiang. 4 strains with cotton wilt pathogen were identified by separation and purification, Koch’s postulate and sequence analysis. 4 fungicides 100 billion/g Bacillus subtilis WP, 8% Ningnanmycin AS, 0.3% Tetramycin AS, 80% mancozeb WP were selected to detect the toxicity for DD64, DD89, DD11 and DD22 pathogenic strains. It was identified that the 4 pathogenic strains were strong pathogenic strains. The results showed that for the DD64 and DD89 in northern Xinjiang, the inhibitory rate of 100 billion/g Bacillus subtilis WP was the best, 96.47% and 95.29% , respectively, followed by 0.3% Tetramycin AS. For the DD11 and DD22 strains in southern Xinjiang, the antibacterial effect of 0.3% Tetramycin AS was the best, 97.91% and 99.35% , respectively, followed by100 billion/g Bacillus subtilis WP. In the toxicity determination of DD64 and DD89, the 8% Ningnanmycin AS had the strongest virulence, and the EC50 values were 0.044 mg/L and 0.046 mg/L, respectively. In production, 0.3%Tetramycin AS is recommended to prevent the expansion and spread of the disease in the early stage. 100 billion/g Bacillus subtilis WP and 8% ingnanmycin AS could be used as rotation agents to effectively control the disease.