Given the increasing burden of chronic diseases in Indonesia, characteristics of chronic multimorbidities have not been comprehensively explored. Therefore, this research evaluated chronic multimorbidity patterns among Indonesians using Indonesian National Health Insurance (INHI) sample data. We included 46 chronic diseases and analyzed their distributions using population-weighted variables provided in the datasets. Results showed that chronic disease patients accounted for 39.7% of total patients who attended secondary health care in 2015–2016. In addition, 43.1% of those were identified as having chronic multimorbidities. Findings also showed that multimorbidities were strongly correlated with an advanced age, with large numbers of patients and visits in all provinces, beyond those on Java island. Furthermore, hypertension was the leading disease, and the most common comorbidities were diabetes mellitus, cerebral ischemia/chronic stroke, and chronic ischemic heart disease. In addition, disease proportions for certain disease dyads differed according to age group and gender. Compared to survey methods, claims data are more economically efficient and are not influenced by recall bias. Claims data can be a promising data source in the next few years as increasing percentages of Indonesians utilize health insurance coverage. Nevertheless, some adjustments in the data structure are accordingly needed to utilize claims data for disease control and surveillance purposes.