We consider an optimal control problem for the hybrid model of a deterministic flow shop system, in which the jobs are processed in the order they arrive at the system. The problem is decomposed into a higher-level discrete-event system control problem of determining the optimal service times, and a set of lower-level classical control problems of determining the optimal control inputs for given service times. We focus on the higher-level problem which is nonconvex and nondifferentiable. The arrival times are known and the decision variables are the service times that are controllable within constraints. We present an equivalent convex optimization problem with linear constraints. Under some cost assumptions, we show that no waiting is observed on the optimal sample path. This property allows us to simplify the convex optimization problem by eliminating variables and constraints. We also prove, under an additional strict convexity assumption, the uniqueness of the optimal solution and propose two algorithms to decompose the simplified convex optimization problem into a set of smaller convex optimization problems. The effects of the simplification and the decomposition on the solution times are shown on an example problem.