Background Multimorbidity has become a new challenge for medical systems and public health policy. Understanding the patterns of and associations among multimorbid conditions should be given priority. It may assist with the early detection of multimorbidity and thus improve quality of life in older adults. Objective This study aims to comprehensively analyze and compare associations among multimorbid conditions by age and sex in a large number of middle-aged and older Chinese adults. Methods Data from the home pages of inpatient medical records in the Shenzhen National Health Information Platform were evaluated. From January 1, 2017, to December 31, 2018, inpatients aged 50 years and older who had been diagnosed with at least one of 40 conditions were included in this study. Their demographic characteristics (age and sex) and inpatient diagnoses were extracted. Association rule mining, Chi-square tests, and decision tree analyses were combined to identify associations between multiple chronic conditions. Results In total, 306,264 hospitalized cases with available information on related chronic conditions were included in this study. The prevalence of multimorbidity in the overall population was 76.46%. The combined results of the 3 analyses showed that, in patients aged 50 years to 64 years, lipoprotein metabolism disorder tended to be comorbid with multiple chronic conditions. Gout and lipoprotein metabolism disorder had the strongest association. Among patients aged 65 years or older, there were strong associations between cerebrovascular disease, heart disease, lipoprotein metabolism disorder, and peripheral vascular disease. The strongest associations were observed between senile cataract and glaucoma in men and women. In particular, the association between osteoporosis and malignant tumor was only observed in middle-aged and older men, while the association between anemia and chronic kidney disease was only observed in older women. Conclusions Multimorbidity was prevalent among middle-aged and older Chinese individuals. The results of this comprehensive analysis of 4 age-sex subgroups suggested that associations between particular conditions within the sex and age groups occurred more frequently than expected by random chance. This provides evidence for further research on disease clusters and for health care providers to develop different strategies based on age and sex to improve the early identification and treatment of multimorbidity.