Large and increasing numbers of rural-to-urban migrants provided new challenges for tuberculosis control in large cities in China and increased the need for high quality tuberculosis care delivered by clinics in urban migrant communities. Based on a household survey in migrant communities, we selected and separated clinics into those that mainly serve migrants and those that mainly serve local residents. Using standardized patients, this study provided an objective comparison of the quality of tuberculosis care delivered by both types of clinics and examined factors related to quality care. Only 27% (95% confidence interval (CI) 14–46) of cases were correctly managed in migrant clinics, which is significantly worse than it in local clinics (50%, 95% CI 28–72). Clinicians with a base salary were 41 percentage points more likely to demonstrate better case management. Furthermore, clinicians with upper secondary or higher education level charged 20 RMB lower out of pocket fees than less-educated clinicians. In conclusion, the quality of tuberculosis care accessed by migrants was very poor and policies to improve the quality should be prioritized in current health reforms. Providing a base salary was a possible way to improve quality of care and increasing the education attainment of urban community clinicians might reduce the heavy barrier of medical expenses for migrants