In order to achieve China’s “30·60” decarbonization goal, the green and low-carbon transformation of the energy system is the fundamental support; the construction of new-type power system is the key step, and the green certificate is the important voucher to reflect the green value of renewable energy. Currently, the distribution mechanism of green certificates in China is oversimplified, which neither effectively measures the variability of green values generated by different types of renewable energy, nor balances the coordinated development of renewable energy. Therefore, to differentiate the exchange mechanism of green certificates by different types of renewable energy power in this paper, an evaluation index system is established, which describes the difference between green certificates, considering the comprehensive value of renewable energy, and an evaluation model is built with the criteria importance by using the intercriteria correlation (CRITIC) method, the entropy weight method, and the technique for order preference by similarity to an ideal solution (TOPSIS) method. Under the development scenario of peaking carbon emissions before 2030, the impact of the differentiated distribution model on the green incomes of centralized photovoltaic distributed photovoltaic power, onshore wind power, and offshore wind power is analyzed. Moreover, the development plan of renewable energy is modified in consideration of the effect of the differentiated distribution model, and policy suggestions on green certificates are proposed accordingly. The results show that the differentiated distribution model of green certificates is practical to provide corresponding decision-making support to the construction and improvement of green certificates trading mechanism in China.