One of the most important steps of the thermal systems design process can be economic optimization. In the conventional methods of this optimization, most of the time system’s availability, amount of production, and maintenance costs are considered to be constant throughout the system’s lifetime. However, factors such as changing of the components’ failure rate due to degradation or repairing, and stops in operation because of overhauls could lead to a change in the availability and the amount of production. Also, in multi-product systems, upstream components’ failures would stop production in downstream parts. In this paper, a method is proposed regarding the consideration of these factors to economic optimization. Hence, the optimal system design and its economic analysis would be more accurate than conventional methods. In terms of a case study, the CGAM cogeneration system is studied. The first step of this optimization is calculating instantaneous availability employing the state-space method by considering the overhauls and time-varying failure rate for the components. Then, the average availabilities for power and heat generation in each year are estimated. As costs and incomes appear to be variables, the net present value of benefits is considered as an objective function and the optimum system properties are achieved through solving the optimization problem.