Abstract Background The rampant urbanization and medical marketization in China have resulted in increased vulnerabilities to health and socioeconomic disparities among the rural migrant workers in urban China. In the Chinese context, the socioeconomic characteristics of rural migrant workers have attracted considerable research attention in the recent past years. However, to date, no previous studies have explored the association between the socioeconomic factors and social security among the rural migrant workers in urban China. This study aims to explore the association between socioeconomic inequity and social security inequity and the subsequent associations with medical inequity and reimbursement rejection. Methods Data from a regionally representative sample of 2009 Survey of Migrant Workers in Pearl River Delta in China were used for analyses. Multiple logistic regressions were used to analyze the impacts of socioeconomic factors on the eight dimensions of social security (sick pay, paid leave, maternity pay, medical insurance, pension insurance, occupational injury insurance, unemployment insurance, and maternity insurance) and the impacts of social security on medical reimbursement rejection. The zero-inflated negative binomial regression model (ZINB regression) was adopted to explore the relationship between socioeconomic factors and hospital visits among the rural migrant workers with social security. Results The study population consisted of 848 rural migrant workers with high income who were young and middle-aged, low-educated, and covered by social security. Reimbursement rejection and abusive supervision for the rural migrant workers were observed. Logistic regression analysis showed that there were significant associations between socioeconomic factors and social security. ZINB regression showed that there were significant associations between socioeconomic factors and hospital visits among the rural migrant workers. Also, several dimensions of social security had significant associations with reimbursement rejections. Conclusions This study showed that social security inequity, medical inequity, and reimbursement inequity happened to the rural migrant workers simultaneously. Future policy should strengthen health justice and enterprises’ medical responsibilities to the employed rural migrant workers.