Background: Multimorbidity not only affects the quality of patients’ lives, but can also bring a heavy economic burden to individuals, families and society. The purpose of this study was to reveal the connections between diseases, especially the important role each disease played in the entire multimorbidity network. Methods: A total of 1,155,734 inpatients were enrolled through multistage stratified random sampling in Jilin Province in 2017. Categorical variables were compared using the Rao–Scott-χ2 test. Weighted networks were adopted to present the complex relationships of multimorbidity. Results: The distributions of the number of diseases differed significantly by gender, age and health insurance scheme (P < 0.001). Diseases of the respiratory system had the highest weight in multimorbidity in young people. Endocrine, nutritional and metabolic diseases and circulatory system diseases were often associated with other systemic diseases in middle aged and old people. Conclusions: Multimorbidity with respiratory system diseases in young people should not be overlooked. Additionally, effective prevention efforts that target endocrine, nutritional and metabolic diseases and circulatory system diseases are needed in middle aged and old people.