Green bond pricing is systematically distorted by the unpriced positive externalities inherent in green projects, leading to market failure and suboptimal investment. This market failure requires government intervention to internalize these externalities, thus correcting the pricing process. Carbon quota operated through market mechanism is a powerful policy tool for this intervention. To correct this, we propose a novel two-stage pricing framework. In the first stage, we develop an optimization model that allocates carbon quotas to a portfolio of heterogeneous green projects. The government’s objective is to internalize externalities by ensuring the Net Present Value (NPV) of each project’s profit stream equals zero while minimizing the use of its scarce carbon quotas. In the second stage, the optimized, discounted streams of revenues and costs are used as the underlying asset value and strike price within Black-Scholes (B-S) model. This approach quantifies the project's equity value by explicitly accounting for future volatility, thus provides a theoretically sound and practically operational method to derive an effective pricing for green bonds, demonstrating how targeted government intervention can restore efficient pricing in the presence of externalities.