Background: Cardiovascular diseases (CVD) are the major cause of work-related mortality from diseases onboard ships in seafarers. CVD burden derives mainly from modifiable risk factors. To reduce the risk factors and the burden of CVD onboard ships in seafarers, it is important to understand the up-to-date prevalence of modifiable risk factors. The primary purpose of this study was to assess the prevalence and clustering of self-reported modifiable CVD risk factors among seafarers. We have also explored the association between socio-demographic and occupational characteristics and reported modifiable CVD risk factor clustering. Materials and methods: A cross-sectional study was conducted among seafarers from November to December 2020 on board ships. In total, 8125 seafarers aged 18 to 70 were selected from 400 ships. Data were collected using a standardized and anonymous self-reported questionnaire. The prevalence value for categorical variables and mean differences for continuous variables were compared using chi-square and independent sample t-tests. Multinomial logistic regression models were performed to identify independent predictors for modifiable CVD risk factor clustering. Results: Out of a total of 8125 seafarers aged ≥18 years on selected vessels, 4648 seafarers volunteered to participate in the survey, with a response rate of 57.2%. Out of 4318 participants included in analysis, 44.7% and 55.3% were officers and non-officers, respectively. The prevalence of reported hypertension, diabetes, current smoking and overweight or obesity were 20.8%, 8.5%, 32.5%, and 44.7%, respectively. Overall, 40%, 20.9%, 6% and 1.3% of the study participants respectively had one, two, three and four modifiable CVD risk factors. Older age (51+ years) (odds ratio (OR): 3.92, 95% confidence interval (CI): 2.44–6.29), being non-officers (OR: 1.36, 95% CI: 1.09–1.70), job duration (10–20 years) (OR: 2.73, 95% CI: 2.09–3.57), job duration (21+ years) (OR: 2.60, 95% CI: 1.79–3.78), working 57–70 h per week (OR: 2.03, 95% CI: 1.65–2.49) and working 71+ h per week (OR: 3.08, 95% CI: 2.42–3.92) were independent predictors for at least two self-reported modifiable CVD risk factor clustering. Conclusion: The results of our study demonstrate that more than four in six (68.5%) seafarers aged between 19 and 70 years have at least one of the modifiable CVD risk factors. Therefore, CVD prevention and modifiable risk factors reduction strategies targeting high-risk groups should be designed and implemented on board ships.