The aim of this study was to analyze the risk factors for the development of type 2 diabetes mellitus (T2DM) with mild cognitive impairment (MCI) and its pathogenesis associated with gut microbiota. A prospective cohort study was conducted to recruit 3820 participants aged 45 years and above who attended health checkups at the checkup center of Linyi City People's Hospital, Shandong Province. A follow-up survey was conducted identifying whether the participant had T2DM as an exposure factor group. Socio-demographic characteristics, blood, urine, and stool samples, lifestyle surveys, dietary status, and neuropsychological tests were collected at baseline and follow-up, exploring the association between clinical characteristics and gut microbiota and the risk for the development of T2DM with MCI.