Description: Background Non-communicable disease (NCD) risk factors can co-exist with disability and cause a greater burden on the health status of adults with disabilities. A lack of egalitarian social policies in China may result in gender disparities in the NCD risk factors of adults with disabilities. However, little is known about the gender disparities in the association between socio-demographics and NCD risk factors among adults with disabilities in China; consequently, we examined this association among adults with disabilities in Shanghai, China. Methods We used the health examination data of 44,896 adults with disabilities in Shanghai in 2014. Descriptive analyses and logistic regression models were conducted to estimate gender disparities in the association between socio-demographics, disability characteristics, and four selected NCD risk factors among adults with disabilities—including high blood pressure, high blood glucose, high blood lipids, and being overweight. We estimated marginal effects (MEs) on NCD risk factors between gender and other confounders. Results Women with disabilities were about 11.6 percentage points more likely to suffer from high blood lipids and less likely to develop the other three risk factors than men were. The association of age group, residence permit, education level, marital status, and disability type with health outcomes varied by gender among adults with disabilities. The difference in age effects between men and women was more pronounced in older age groups. Urban residence was associated with less risk of high blood pressure risk among women (ΔME =  − 0.035, p