Considering the service characteristics and negative impact resulted from the undesirable output of public transport, taking the public transport operation systems of thirty-five large and mediumsized cities in China as empirical samples, an evaluation model of the service effect and operational efficiency of public transport was established based on Slack Based Model and Data Envelopment Analysis (SBM-DEA) method. A conclusion is summarized that considering undesirable output has significant impact on the operational efficiency evaluation of public transport. The average value of the service effect and operation efficiency of public transport are 0.61, 0.64, which decline by 6.2%, 7.2% compared with the values of these without considering undesirable output. The overall efficiency of public transport in large and medium cities in China still needs improving. Implementation of differentiated demand management strategies, development of clean energy vehicles and strengthening the supervision of public transport services are the key points to improve efficiency.