The prevalence of multimorbidity tends to increase with age, but it is now also reported in the middle-aged population, which has a negative impact on healthcare systems and health outcomes. This study aims to analyze the patterns and factors associated with multimorbidity in Indonesia. This national cross-sectional population-based survey used publicly available data from the Indonesian Family Life Survey (IFLS-5) for 2014 among middle-aged (40-59 years old) and elderly (≥ 60 years old) respondents. Information on all chronic diseases was assessed using a self-reported questionnaire. Sociodemographic and health-related behavioral factors were obtained from self-reported data. Binary logistic regression analysis was used to identify the factors associated with multimorbidity. Adjusted odds ratios (AORs) with 95% confidence intervals (CIs) were reported. The study recruited 11,867 respondents. The prevalence of multimorbidity was 18.6% (95% CI 17.9-19.3) with which 15.6% among middle age (95% CI 14.95-16.25) and 24.9% among the elderly (95% CI 24.12-25.68). Hypertension was the most commonly reported disease (23.2%) in all combinations of multimorbidity and among all age groups. Socio-demographic factors: elderly (AOR: 1.66; 95% CI 1.46-1.89), female (AOR: 1.42; 95% CI 1.20-1.69), living in the urban area (AOR: 1.22; 95% CI 1.09-1.38), higher educational level (AOR: 2.49; 95% CI 1.91-3.26), unemployed (AOR: 1.63; 95% CI 1.44-1.84), and higher economic level (AOR: 1.41; 95% CI 1.18-1.68) were associated with multimorbidity. Poor health behavior factors: being former smokers (AOR: 2.03; 95% CI 1.65-2.51) and obesity (AOR: 1.53; 95% CI 1.35-1.75) were also associated with multimorbidity. The prevalence of multimorbidity in the middle-aged and elderly population in Indonesia is relatively high, particularly in populations with poor health behaviors. Therefore, healthcare professionals should integrate more patient-specific factors when designing and implementing tailored interventions to manage multimorbidity in Indonesia.