The prevalence of non-communicable diseases is increasing worldwide. Multimorbidity and long-term medical conditions is common among these patients. This study aimed to investigate the patterns of non-communicable disease multimorbidity and their risk factors at the individual and aggregated level. Data was inquired from the nationwide survey performed in 2011, according to the WHO stepwise approach on NCD risk factors. A latent class analysis on multimorbidity components (11 chronic diseases) was performed and the association of some individual and aggregated risk factors (urbanization) with the latent subclasses was accessed using multilevel multinomial logistic regression. Latent class analysis revealed four distinct subclasses of multimorbidity among the Iranian population (10069 participants). Musculoskeletal diseases and asthma classes were seen in both genders. In males, the odds of membership in the diabetes class was 41% less by increasing physical activity; but with increased BMI, the odds of membership in the diabetes class was 1.90 times higher. Tobacco smoking increased the odds of membership in the musculoskeletal diseases class, 1.37 and 2.30 times for males and females, respectively. Increased BMI and low education increased the chances of females' membership in all subclasses of multimorbidity. At the province level, with increase in urbanization, the odds of membership in the diabetes class was 1.28 times higher among males (P = 0.027). Increased age, higher BMI, tobacco smoking and low education are the most important risk factors associated with NCD multimorbidity among Iranians. Interventions and policies should be implemented to control these risk factors.