Tobacco control intervention with Chinese internal migrants, especially those working in factories has rarely been investigated. This study aims to identify aids and barriers to implementing a comprehensive pilot intervention aimed at reducing smoking among migrant workers working in factories in China. Twenty in-depth interviews were conducted 3 months into the intervention, with managers, migrant workers and team leaders in two factories, where the pilot intervention was implemented, in Zhongshan city in Guangdong, a southern Chinese province. Data analysis was based on the thematic approach. This study identifies the societal, individual and programmatic factors that could influence the implementation of a pilot smoking cessation intervention among migrant workers in the two Chinese factories. At the societal level, social customs and relationships where smoking is seen as essential in social communications was the most important barrier to the implementation of smoking cessation intervention. At the individual level, migrant-related features such as low education, high mobility and poor integration with local residents, together with poor health beliefs and attitudes added to the challenges of implementing smoking cessation intervention. At the programmatic level, the role of small-team leaders was generally positive, although limited due to their busy work patterns and poor powers of enforcement. Achieving successful smoking cessation intervention in factories could be challenging with many migrants, as multi-level factors including social context, intervention delivery, individual and migrants' characteristics play an important role in shaping the implementation of the intervention. Our study suggests the importance of tailoring interventions for the migrant factory workers. ChiCTR-OPC-17011637 at Chinese Clinical Trial Registry. Retrospectively registered on 12th June 2017.