To explore the factors affecting the stability of bus routes and the corresponding evaluation methods, and to accurately improve the service quality and passenger attractiveness of bus routes, focusing on the volatility of the passenger waiting time and the entire travel time, this paper proposes a classification method for the operation instability of bus routes. By taking Shanghai as an example, 135 bus routes in the central city and Jiading new city were selected and divided into 4 types to carry out application research. It is found that the proportions of routes with two “good” indicators and two “bad” indicators in the central city and Jiading new city are basically the same, and are not affected by spatial location. However, the routes with one “good” indicator and one “bad” indicator show differences. The 4 types of routes were then profiled twice by using several indicators such as length of route, distance between bus stops, ridership per 100 kilometers per day, the nonlinear coefficient of routes, the mileage ratio of bus lane, the mileage ratio of the main roads, the population density along the route, the POI density along the route, and so on. By combining the results of twice profiles and considering the spatial location differences between the central city and Jiading new city, targeted optimization strategies, such as operation scheduling optimization, additional bus lanes and main road improvement in new city, were proposed. This research can provide decision support for accurately improving the service quality of bus routes.