The retrofit of heat exchanger networks (HENs) is very important to high-energy consumption enterprises for saving energy, protecting the environment, and improving their market competitiveness. It is also an important branch of heat integration research. The retrofit of HENs is more difficult than grassroots design because of the greater number of constraints. In this paper, the novel mathematical model for HEN retrofit is based on the stepwise superstructure model from Yee et al. The existing heat exchangers and structures are applied fully in the retrofitted HEN, and the modification cost is decreased with energy saving. The hybrid genetic algorithm is used to solve the mixed integer nonlinear program problem. Two examples are given to show the improved effect of the novel retrofit method with the minimum of the total cost of new heat exchangers and newly added areas of the existing heat exchangers and repiping and utilities.