Background: Few studies have investigated nutritional and genetic factors and their interactions on noncommunicable diseases (NCDs) among Chinese adults. Objective: The Nutrition and Health in Southwest China (NHSC) study investigates the impact of diet, lifestyle, genetic background, and their interactions on NCDs among adults in Southwest China. Methods: This prospective cohort study, initiated in winter 2013, completed baseline data collection in December 2018, with 2-year follow-ups. Data includes genomics, anthropometry, nutrition, eating behaviors, physical activity, depression, mental disorders, clinical and biochemical examinations, and lifestyles. Results: 7926 adults completed the baseline questionnaire. Analyses suggested associations between dietary energy density and BMI, and between dietary glycemic index/load or serum 25(OH)D and glucose homeostasis. Less television time and healthy eating patterns may influence cellular aging. Conclusions: The NHSC cohort provides valuable data for investigating gene-nutrition-lifestyle interactions on NCDs among Southwestern Chinese adults.