Abstract: 【Objective】 Since 2015, a so-called stiffness and cracking boll has occurred in cotton fields of Xinjiang, which has caused a great impact on the yield and quality of cotton. So, experiments were carried out to ascertain the cause. 【Methods】 The key factor that caused stiffness and cracking cotton bolls in Xinjiang were revealed by distinguishing the symptoms of previouslyreported boll rot disease. In order to find out whether F. intonsa and A. gossypii were harmful, these symptoms were observed by the method of nylon mesh cover for worm-wearing. In order to find out whether the pathogen was infected, the samples were collected in the cotton fields of northern and southern Xinjiang, and their pathogens were isolated, purified and identified. At the same time, the harm of cotton aphid and the relationship between stiff boll and cracking boll were preliminarily investigated. 【Results】 The main cause of rust-colored markings on the boll surface of cotton in fields in Xinjiang was F. intonsa. although the simple harm of cotton aphid did not directly from the symptoms of stiffness and cracking bolls, its harm and the resulting wound and its secretion could obviously induce weak parasitic bacteria such as Alternaria spp. and Cladosporium spp. infection and growth, and lead to the occurrence of dark brown or olive green stiffness and cracking bolls in cotton fields of Xinjiang. 【Conclusion】 The main cause of rust-colored markings on the boll surface of cotton in fields in Xinjiang was F. intonsa.