In this study, nonlinear control of high duty counter-current heat exchanger is considered. The dynamics of this system can be captured by first order hyperbolic partial differential equations (PDEs), which are stiff due to the high rate of heat transfer. The potential of multi-time scale dynamics is discussed, and model reduction is performed using singular perturbations to obtain non-stiff PDE models which are valid in each time scale. Three controllers are designed and compared in the simulation case study: input/output linearizing controllers on the basis of original model and reduced order model, and a proportional-integral controller. The nonlinear controller designed using the reduced order model showed a superior performance compared to the others, especially in the presence of large modeling errors and disturbances.