To improve the operational service capacity of flex-route transit under uncertain travel demand, a slack arrival strategy and a meeting point strategy were proposed. First, the operating mechanism of flex-route transit service under the proposed strategies was described in detail, and the process was divided into a two-stage optimization problem. Then, mixed integer programming (MIP) was employed to formulate the problem with a twofold objective: to maximize the number of accepted requests in the first stage and to minimize the total trip time of the accepted passengers in the second stage. A memetic algorithm was proposed to solve the model in a reasonable amount of time. Simulation experiments based on a real-life flex-route transit service were conducted to evaluate the proposed strategies. Results show that the two strategies, which relaxed the departure time constraints of checkpoints and the space constraints of reserved pick-up and drop-off locations, could improve the routing flexibility of flex-route transit service and significantly reduce the passenger rejection rate without any additional operating cost. Besides, when the two strategies were applied at the same time, the rejection rate could be reduced by up to 22%.