Heat exchangers are one of the most important thermal devices. Shell and tube heat exchangers are the common types of heat exchangers and sustained a wide range of operating temperature and pressure. Modeling and controlling heat exchanger system is a difficult assignment because of its nonlinearity. As the flow rates changes, the gain, time delay and time constant varies, hence causing system nonlinearity. The solution for such problems is finding acceptable mathematical model and design a controller which provides better performance indices. In this paper mathematical model (experimental or empirical based) to represent the real system and design suitable controller which remove the offset and settle fast with minimum steady state error has been proposed. To this end, system model design the Proportional-Integral-Derivative controller for shell and tube heat exchanger using Ziegler Nichols method, Cohen-coon method and Chein et al. method. Since two opposing dynamic effects are existing in the system and has a problem of dynamics of inverse response and large overshoot. Therefore, Chein et al. tuning method have better performance than that of the others. In case of Chein et al. the overshoot of 2.577 % and settling time of 63.1 s.