This work addresses the output regulation of flow systems described by a class of nonlinear partial differential equation (NPDE) systems with either one or two manipulated inputs. The main design procedures involves two steps, the first is to determine the feasible steady-state operation through the numerical computation, the second is to use the 'boundary' controls whose number and position can be directly planned. The developed control strategy can be treated as a typical linearization design, so that the outlet state of flow systems can be approximately linearized and maintain a certain degree of output tracking performance. Since the inlet perturbations may cause the hot spot phenomenon or open-loop instability of nonisothermal processes, the special two-point control scheme can suppress the effect of inlet disturbances and alleviate the control action. Finally, several issues are evaluated through simulations and implemented on an exothermic plug-flow reactor (PFR).