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Increasing the efficiency of bus transit remains to be a challenge of urban transportation. Since the optimization of bus routes and their frequencies is significant for transit efficiency, this study aims to develop two data envelopment analysis (DEA) models using network epsilon-based measures (NEBMs). The first NEBM model adopts twelve indicators to evaluate the rationality of the route network design; the second NEBM model uses nine indicators to evaluate the efficiency of the frequency setting. Both NEBM models can simultaneously consider radial and nonradial inputs and outputs and dig into details of the 'input/output transformation box.' Finally, the bus transit system of Nanjing in China is used as a case study. Results show that the overall efficiency of network route design is higher than that of frequency setting. According to comparisons between descriptive statistics of the top and bottom performers, inefficiency causes of bottom performers are identified and corresponding improvement measures are suggested. The proposed models are helpful for the development of bus transit systems and can be applied on a yearly/monthly basis., 1. Introduction A high-quality bus transit system will attract urban citizens to use, which furthermore helps to alleviate traffic congestion, reduce air pollution, and promote social fairness. Given growing needs [...]