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To solve the problems of bus bunching and large gaps, this study combines bus holding and speed adjusting to alleviate them respectively considering the characteristics of passenger’s perceived waiting time. The difference between passenger’s perceived waiting time at stops and actual time is described quantitatively through the expected waiting time of passengers. Bus holding based on a threshold method is implemented at any stops for bunching buses, and speed adjusting based on a Markovian decision model is implemented at limited stops for lagging buses. Simulations based on real data of a bus route show that the integrated control strategy is able to improve the service reliability and to decrease passengers’ perceived waiting time at stops. Several insights have been uncovered through performance analysis: (1) The increase of holding control strength results in improvement of the headway regularity, and leads to a greater perceived waiting time though; (2) Compared to traveling freely, suitable speed guidance will not slow down the average cruising speed in the trip; (3) The scale of passenger demand and through passengers are the two key factors influencing whether a stop should be selected as a speed-adjusting control point.