Background Coal workers are inclined to report multi-site work-related musculoskeletal disorders (WMSDs) due to their specific working environment and extensive exposure to occupational hazards, which seriously affect the physical and mental health of coal workers. objective To investigate the prevalence of multi-site WMSDs among workers in coal mining enterprises in Xinjiang, and analyze the related factors influencing multi-site WMSDs. Methods Using stratified cluster random sampling method, Musculoskeletal Disorders Questionnaire, Job Burnout Questionnaire, and Brief Occupational Stress Questionnaire were distributed in six Xinjiang coal mining enterprises to collect data on general information, prevalence of WMSDs in the past year, work-related information, job burnout, and occupational stress among coal miners with a working experience ≥ 1 year. A multiple logistic regression model was used to analyze the influencing factors of multi-site WMSDs. Results A total of 1730 questionnaires were distributed in this survey, 1448 valid questionnaires were recovered, and the valid recovery rate was 83.7%. Among the 1448 coal miners, 93.2% were males and 6.8% were females; 39.2% were aged ≤ 35 years, 31.1% were aged 35-45 years, and 29.6% were aged > 45 years; 58.4% reported ≤ 10 years of working experience, 20.0% reported 10-20 years, and 21.6% reported > 20 years. The total prevalence rate of WMSDs in the coal miners was 75.6% (1095/1448), the prevalence rate of multi-site WMSDs was 58.4% (846/1448), and the prevalence rate of one-site WMSDs was 17.2% (249/1448). The results of multiple logistic regression analysis showed that working experience > 20 years (OR=2.245, 95%CI: 1.655-3.045), severe burnout (OR=2.644, 95%CI: 1.549-4.516), and multiple repetitive operations per minute very often (OR=2.038, 95%CI: 1.339-3.101), often bending at larger angles (OR=1.467, 95%CI: 1.111-1.938), long-time bending the neck forward (OR=1.671, 95%CI: 1.294-2.159), and slipping or falling down (OR=2.459, 95%CI: 1.908-3.168) were positively correlated with multi-site WMSDs; sufficient rest time (OR=0.718, 95%CI: 0.565-0.913) was negatively correlated with multi-site WMSDs. Conclusion Multi-site WMSDs is common among workers in coal mining enterprises, and the prevalence rate of multi-site WMSDs is higher than that of one-site WMSDs. Working experience, job burnout, frequent multiple repetitive operations per minute, often bending at larger angles, long-time bending the neck forward, slipping or falling down, and sufficient rest time are influencing factors of multi-site WMSDs in coal workers.