Bus bunching is a critical issue in bus operation management. This study investigated the impacts of potential factors affecting bus bunching on a city-wide bus route network, using Taipei City as an example with its 267 bus routes and 4741 bus stops. Frequency of bus bunching was measured on an hourly basis using Automatic Vehicle Location data. Multilevel count models based on Conway-Maxwell Poisson distributions were developed, and the spatiotemporal distributions of random intercepts and residuals were examined. The results showed that the effects of bus lane design, bus route network and operation, and traffic characteristics were consistent with those reported in prior studies. However, a quadratic relationship between bus route length, best measured by number of stops, and bus bunching was identified, which explains the conflicts between the theories of bus bunching propagation and self-repair. Bus route design often faces a dilemma between extending route length to collect additional passengers and reducing in-vehicle travel time to enhance service quality. The findings of the study could be a useful reference for bus route design to minimize bus bunching.