A two-echelon green supply chain system with one green manufacturer and one capital-limited retailer was considered on the basis of random demand, then the optimal decision-making problem of the members when the manufacturer and the third-party bank respectively provided the credit loans was studied. Moreover, a punishment mechanism was introduced, and its impact on the operational efficiency of the green supply chain system was studied. Finally, the impact of unit punishment on optimal decisions and profits was analyzed through numerical examples. The research results show that the retailer with capital-limited is more inclined to choose the credit loans that provided by the manufacturer, and the introduction of the punishment mechanism has effectively improved the efficiency of system operation.