Multidrug resistant tuberculosis (MDR-TB) has attracted increasing attention in achieving the global goal of tuberculosis (TB) control. China has the second largest TB burden worldwide and has been experiencing large-scale domestic migration. This study aims to explore the effect of migrants on non-adherence to MDR-TB treatment. A cross-sectional study was carried out in Wuhan, China. The exposure cases were migrants who were not locally registered in the residence registration system. The control cases were local residents. Non-adherence cases were patients who were lost follow-up or refused treatment. Chi-square and t-test were used to compare variables between migrants and local residents. Logistic regression models using enter method were used to determine the relationship between migration and non-adherence to treatment. Moderation and medication effects on the association between migrant status and non-adherence were also explored. We studied 73 migrants and 219 local residents. The migrants, who did not to adhere to treatment (55, 75.3%), was far higher than that of local residents (89, 40.6%). Migrants with MDR-TB had 10.38-times higher difficulty in adhering to treatment (adjusted OR = 10.38, 95% CI 4.62-25.28) than local residents. This additional likelihood was moderated by age and treatment registration group. Migration had an indirect association with non-adherence to treatment via social medial insurance (adjusted OR = 1.05, 95% CI 1.01-1.13). There a significant increased likelihood of non-adherence to treatment among migrants with MDR-TB, highlighting the importance of improving treatment adherence in this population. Migration prevented migrants from gaining access to social medical insurance and indirectly reduced their likelihood of adherence to treatment.