Background: On-the-job training is an important strategy for general practitioners to deliver appropriately community health services in China. The development of basic professional competence for general practitioners is the main goal of on-the-job training program. The aim of this study was to explore the needs of and the challenges to on-the-job training for general practitioners, and to provide advices for policy-makers to carry out this program more effectively. Methods: We conducted 3 nominal group techniques, 17 in-depth interviews and 3 focus groups to identify the status of, needs of and challenges to on-the-job training for general practitioners in Liaoning, Ningxia, and Fujian provinces from September 2011 until December 2011. Audiotapes and transcripts were analyzed to identify major themes. Content analysis of the data was completed from January 2012 to March 2012. Results: Basic theoretical knowledge and clinical skills were the main needs for general practitioners during on-the-job training. The challenges during training included the time contradiction between work and training, deficiencies of qualified preceptors, and lack of training funds. Participants gave recommendations how to resolve the above problems. Conclusions: In order to improve the outcomes of general practice on-the-job training, it is necessary for government officials to resolve the contradiction between work and training, train preceptors continuously, and increase financial support in the training program.