With the acceleration of urbanization and the continuous improvement of people’s living standards, people rely more and more on cars to travel, resulting in serious traffic congestion. We need to promote the development of regular transit to alleviate traffic congestion, and the use of public transport is mainly concerned about the punctuality of its operation. This paper takes the characteristics of the bus operation as the research object, it analyzes the punctuality rate of the bus operation by collecting the real-life traffic data of the Nanjing Bus Line 3, and analyzes the factors that affect the punctuality performance of the bus operation. The results show that, the time periods, whether to set up bus lanes, the distance of the adjacent stops have a greater impact on the punctuality rate of the bus operation. Finally, proposing suggestions to improve the punctuality rate of the bus operation.