As a mode of green transport that can effectively alleviate urban traffic congestion and improve air quality, bus transport is highly subsidized by governments at all levels in China. Thus, measuring efficiency in the bus transport sector is particularly important. However, few reports in the literature have taken exogenous environmental factors into consideration to evaluate public transport operation efficiency. This may lead to inaccurate evaluation results. This study employs the three-stage DEA model, which can eliminate the impacts of exogenous environmental factors on public bus transport operation to gain real efficiency results. Meanwhile, to further explore how exogenous environmental factors affect bus transport operations, a tobit model is used to analyse the results. The main results of this paper reveal the following: first, exogenous environmental factors have a significant impact on the operational efficiency of bus transport. It is reasonable and necessary to select the three-stage method to eliminate environmental factors for real bus operation efficiency. Second, the fluctuations of the bus transport efficiency of 30 cities decreased during 2010–2016. The western region has the highest operation efficiency, followed by the eastern and the middle regions. Third, the economic, taxi transport, and urban rail transport have a marked impact on the operational efficiency of bus transport. This paper confirms the important influence of exogenous environmental factors on the efficiency of public transport operations. In addition, this article could help improve the efficiency of urban public transport operations and promote the attractiveness of urban public transport and the amount of green travel.