Intermodal transfer time is one of the most significant components of transit travel from the perspective of passengers. Even in a well-coordinated transit network, operational control is necessary to maintain the coordinated transfers that may be disrupted because of unexpected delays of transit vehicles. Connection protection (CP) involves holding a transit unit to wait for another transit unit that is planned to provide a timed transfer but has been delayed. This study proposes a strategy for CP that predicts how the controlled transit unit affects the waiting times of related passengers and determines whether the unit should be held to preserve the connection based on passenger waiting times. The strategy is evaluated with a developed simulator that models transfers from a commuter rail line in the city of Brampton, Canada, to a local bus route. The proposed strategy is compared with two extreme strategies: holding the bus until the train's arrival and operating it without any holding. Results show that the proposed strategy improves transfer efficiency and reduces the waiting times of affected passengers.