The various functional aging behaviors within electrochemical energy storage (EES) are important factors affecting EES planning decisions and economic evaluations. First, a two-stage capacity optimization decision model for EES is proposed considering functional decay to address the capacity allocation issue of EES participating in both the electrical energy and frequency modulation markets in an independent operational mode. The first stage model optimizes the allocation of EES capacity with the goal of maximizing benefits within the expected life cycle of the EES; the second stage model optimizes the EES operational decisions within each operating year with the goal of maximizing daily operating profit considering the constraints of EES lifespan and functional aging behavior. Then, the configuration capacity and expected lifespan of EES in an independent operational mode is obtained using the multi-parameter programming theory method to jointly optimize and analyze the two-stage model. Finally, the impact of functional aging behavior of EES on its economic life and capacity configuration is analyzed through numerical simulation and the effectiveness of the proposed model and method is verified.