Cotton diseases caused by soil-borne pathogenic fungi present a major constraint to cotton production not only in China but also worldwide. A long-term field inventory was made of the prevalence of Fusarium and Verticillium wilt of cotton in the Jiangsu coastal area of China from 2000 to 2014. Various factors (crop varieties, rotation and weather) were analyzed to explore the dynamics of these diseases in cotton. The results showed that the prevalence of Fusarium and Verticillium wilt increased before 2005 and that Verticillium wilt remained at a high incidence over most of the past 10 years, while Fusarium wilt began to gradually decrease after 2005. The dynamics of Fusarium and Verticillium wilt were closely associated with the introduced cotton varieties and the intensive cropping history. In addition, weather conditions occurring during some of the years appeared to coincide with a substantial variation in the wilt diseases. Our study highlighted epidemiological dynamics of Fusarium and Verticillium wilt in a long-term survey.