Increased drug resistance rates to the first-line anti-tuberculosis drugs and multidrug resistance (MDR) were observed in China. The objectives of this study were to determine the prevalence and risk factors for drug-resistant tuberculosis (TB) in urban China and, more specifically, to determine the contribution of migration to case burden and drug resistance rates of urban cities. A facility-based epidemiological study of all active TB patients reported in the four districts of Shanghai and Ningbo between April 1, 2008 and March 31, 2009 was conducted. Residents had significantly higher drug-resistance rates than migrants (any drug resistance: 29.8% vs. 23.5%, respectively, P = 0.038; MDR: 10.9% vs. 6.1%, P = 0.048). Previously treated migrant patients were more likely to harbor drug-resistant TB and MDR-TB than new migrant cases, with adjusted odds ratios of 3.85 and 6.52, respectively. In total, 46.2% of the previously treated cases were resistant to INH, 38.5% to SM, 33.3% to RMP and 30.8% to EMB, while 13.1%, 17.5%, 7.0% and 6.8% of new cases were resistant to the four agents, respectively. To prevent the transmission of drug-resistant TB among migrants and residents, improved case management and appropriate treatment regimens should be sustained to prevent acquired drug resistance.