In this paper, by using a distributed control system (DCS) device, a robust tracking control system is proposed based on robust right coprime factorization for a heat exchanger actuated by a water level process with coupling effects and uncertainties. Firstly, nonlinear models of water level and temperature processes with coupling and uncertainties are given. Secondly, nonlinear feedback tracking control systems corresponding to a multi-input multi-output (MIMO) process are realized by using operator-based robust right coprime factorization. Meanwhile, stability of the control systems is guaranteed by using robust stability conditions compatible with the MIMO process including coupling effects, and to improve the output tracking performance, tracking controllers are designed. Finally, the effectiveness of the proposed design scheme is confirmed by simulation and experimental results.