In order to promote the development of new energy buses more smoothly, a random survey of public perception on new energy vehicles and willingness to pay for new energy bus fares is conducted in four first-tier cities in China. We design two sets of questions in the survey and adopt a sample selection model to correct the possible sample selection bias in the estimation of willingness-to-pay for new energy fares. The results show that firstly in the zero willingness to pay samples, very few of them are with genuine zero, the others all being protest respondents. Second, the sample selection model indicates that the sample selection bias is positively significant in the estimation of willingness to pay. Third, income, peoples knowledge about new energy vehicles, the degree of recognition of the role of new energy vehicle in improving urban air quality, and views on air quality influence willingness to pay more for new energy bus fares positively. We propose that pricing new energy bus fares higher is reasonable and more knowledge concerning new energy vehicles should be disseminated to the public.