As an energy efficient technology that generates electricity and captures the heat that would otherwise be wasted to provide useful thermal energy, combined heat and power (CHP) hybrid energy systems have been widely used in the U.S. In the presented study, a two-stage co-design optimization model for CHP-based hybrid energy systems is developed. By applying a mixed integer programming (MIP) method, the optimization is performed from the operational and design perspectives. Six components: CHP, boiler, heat recover unit (HRU), thermal storage system (TS), power storage system (ES), and photovoltaic (PV) are considered in the CHP-based microgrids. During the optimization process, the cost-based optimal component design solutions are firstly obtained by minimizing the total installation costs of the components. The optimal operational strategy is further attained based on the component design by minimizing the costs from production, operation and maintenance, startup, and unsatisfied load. In the end, non-disruptive and disruptive scenarios are considered in the case study to testify to the model’s effectiveness in co-design and reliability improvement.