A two tank Continuous Stirred Tank Reactor (CSTR) is a typical chemical reactor system with highly non-linear characteristics where an efficient control of the product concentration in CSTR is achieved only through an accurate model. The dynamic model of the process is developed for a complex reaction system. A Fuzzy logic controller strategy is developed for a two tank continuous reactor system, which has high nonlinearity and wide operating range for a complex reaction system and it is compared with IMC based PID controller to control product concentration of the CSTR. Simulation studies have been carried out in MATLAB SIMULINK. The best controller has been chosen by comparing the criteria of response such as settling time, rise time, percentage of overshoot and steady state error. From the simulation studies, the Fuzzy controller has better performance than the conventional PID controller.