The concept of level of service (LOS) is meant to reflect user perception of the quality of service provided by a transportation facility or service. Although the LOS of bus rapid transit (BRT) has received considerable attention, the number of levels of service of BRT that a user can perceive still remains unclear. Therefore, in this paper, we address this issue using fuzzy clustering of user perception. User perception is defined as a six-dimension vector of the perceived arrival time, perceived waiting time, bus speed perception, passenger load perception, perceived departure time, and overall perception. A smartphone-based transit travel survey system was developed, with which user perception surveys were conducted in three BRT systems in China. Fuzzy C-Means clustering, improved using a simulated annealing genetic algorithm, was adopted to partition user perception into two to ten clusters. Seven cluster validity indices were used to determine the appropriate number of LOS categories. Our results indicate that users can perceive two to four levels of service.