Objective This study was to identify factors limiting the implementation of smoking policies in county-level hospitals. Methods We conducted qualitative interviews (17 focus groups discussions and 6 one-to-one in depth interviews)involving 103 health professionals from three target county-level hospitals. A combination of purposive and convenience sampling was used to recruit subjects and gain a broad range of perspectives on issues emerging from ongoing data-analysis until data saturation occurred. The transcripts were analyzed for themes and key points. Results The main themes that emerged suggested that both smokers and non-smokers viewed smoking very negatively. However, it was clear that, underlying this acceptance of the health risks of smoking, there was a wide range of beliefs. Most of the health professionals pointed out that, as smoking was legal, addictive, and influenced by social norms, currently it was almost unrealistic to expect all smokers to give up smoking or not to smoke in the hospitals. Furthermore, they were concerned about the potentially detrimental effects of providing counseling advice to all smokers on the interpersonal relationship among colleagues or between doctors and patients. In addition, low level of employee participation influenced the sustainable implementation of smoking policies. Conclusions Simply being aware of the health risks about smoking did not necessarily result in successful implementation of the smoking policies. Application of comprehensive intervention strategies such as implementing smoking policies in public places at the county level, creating supportive environments, promoting community participation,and conducting health education, may be more effective.