Occupational stress, cumulative fatigue, and work-related musculoskeletal disorders (WMSDs) are major concerns in the field of occupational health. Previous studies on occupational health focused on key industries, such as medical care, while there were few related studies on Information Technology (IT) industry. Our study explored the factors influencing occupational stress, cumulative fatigue, and musculoskeletal disorders in the IT industry. We collected 1363 IT workers’ valid questionnaires, of which 73.1% of participants were technicians in Chongqing, 2021. The core occupational stress scale (COSS), self-diagnosis checklist for the assessment of workers’ accumulated fatigue and Chinese musculoskeletal disorders questionnaire were used to measure the occupational stress, cumulative fatigue, and musculoskeletal disorders of the respondents. Logistic regressions were used to explore the correlated factors affecting these indicators. The results showed that the prevalence of occupational stress, cumulative fatigue, and musculoskeletal disorders was 50.4%, 47%, and 72.3%, respectively. Working in the current position for 3–10 years was a common increased risk for all three indicators. Insomnia was associated with an increased risk of cumulative fatigue (Odds Ratio, OR = 2.156, p < 0.001) and musculoskeletal disorders (OR = 1.878, p < 0.001). Cumulative fatigue was also associated with an increased risk of having WMSDs (OR = 3.207, p < 0.001). According to our findings, occupational factors, such as long working years, overtime work, and personal lifestyle, are highly related to the occurrence of occupational stress, cumulative fatigue, and musculoskeletal disorders for IT industry workers. More attention should be paid to women and those with long working hours in the IT industry.