There is currently a “mother-daughter” model for hydrogen refueling stations (HRS). On-site “mother” stations produce hydrogen from city natural gas or water electrolysis, and off-site “daughter” stations are supplied with hydrogen from nearby on-site stations. This HRS system is a micro hydrogen supply chain that includes hydrogen suppliers, retailers, and end consumers characterized via demand functions. The present paper designs an optimal business model for this distributed HRS system using a multi-level game model, given that on-site and off-site HRS can operate individually or as a coalition to supply hydrogen. Stackelberg game and Shapley value models are constructed to explore how cooperative operation is superior by generating more profits than separate operation. Accordingly, in order to promote cooperation between on-site and off-site operators of HRS, an evolutionary game model is developed to investigate the allocation of profits and coordinated costs on the equilibrium of cooperative operation. The authors conclude that boosting the initial probabilities of actors to choose cooperative strategies and decreasing the coordinated cost can lead the game system to the ideal consequence. The present paper offers recommendations including establishing regulation standards for HRS operation, and advancing the information technology to design a more effective cooperative mechanism.