This paper presents the mixed-integer linear programming (MILP) based model to approach the admission control in flow shop scheduling problem with queue time constraints, where there are various upper bounds limit in each queue. The scheduling proposed in this paper iteratively retrieves the real-time status of a production system such as machine failures and recoveries, and job arrivals in each step and generate the most updated scheduling result at each decision time. Our objective function is to minimize the occurrence of queue time violation. We solve the MILP using combinatorial Benders’ cut (CBC), where the MILP model is decomposed into two independent parts: the binary variables as a master problem and the continuous variables as a slave problem. We compare the CBC with the results gained from the CPLEX. The numerical results indicate that the CBC indeed effectively and efficiently reaches the good feasible solution within a reasonable timeframe in the context of timely updating scheduling problem.