In this paper, a rigorous mathematical model of multistage flash system (MSF) is presented based on a detailed physicochemical representation of the process, including all the fundamental elementary phenomena. In particular, Comparison to the mathematical model of reference, two integer variables, which are the number of recovery stage (NR) and the number of rejection stage (NJ), are introduced to the model. Additionally, two special variables, which are the ratio of recirculation brine water flow rate and distillation flow rate and the ratio of make-up flow rate and the distillation flow rate, are introduced to the model as the continuous variables too. Then, the MSF system is described as a mixed-integer nonlinear programming (MINLP). The objective is to minimize the total annual cost (TAC), which is mainly composed of the operating costs and investment cost. Here the modified genetic algorithm (MGA), which is characterized as mixing coding way, is adopted for the system optimization. A case study and a discussion of the results are presented.