Abstract: Cotton wilt syndrome is a new disease of Shanxi Province, cotton-growing areas in recent years, so far only a superficial investigation report and pathogen report, the lack of basic understanding of its fluctuation and influencing factors. The aim was to present the comprehensive management methods and measures of the cotton wilt syndrome. Adjacent contrast methods of cultivation, observation year incidence of seed strains and normal strains of seed was the same strain or material before onset of the severity of and sooner or later. The results showed that, the incidence of strains of seed offspring than its homologous normal seed time of onset as early and morbidity strain rate, that the disease was not the incidence of strains of seed genetic disease. By adjacent contrast to cultivation of genetically modified varieties and their non-transgenic parental cultivars, and then planted a large number of other non-transfer genetic material observed, the results showed switch to genetically modified varieties incidence more while its parent varieties incidence rarely, certain varieties of differences to reach a very significant with, non-genetically modified material no cases had been seen. That might be associated with cotton genetically modified material related to the occurrence of disease. The fitting analysis through the cotton wilt syndrome observed data and the local meteorological observation data, the results showed the occurrence of disease might be associated with less rainfall, relative air humidity was low, evaporation larger; through the analysis of climate observations and test field might also be ground in the cotton fields plastic film≥40℃the number of days more relevant.