Water option trading aims at solving the problem of uneven spatial and temporal distribution of water resources. With the change of global climate, rainfall has become an important factor leading to the uneven spatial and temporal distribution of water resources. In this paper, Markov chain is used to divide and forecast the rainfall scenarios. On the basis of rainfall forecast, the related costs of water option trading are determined. The forecast results of rainfall index are integrated into the determination of the ultimate overprice of water options. The improved Black-Scholes option pricing model is used to determine the rights of water options trading based on the forecast results of rainfall. Finally, the rationality of the calculation results is verified by using the extended linear expenditure model, which proves the rationality of the transaction price determined by the model. Taking Guangdong province as an example, this paper verifies the necessity of incorporating rainfall index into water option trading and the rationality of the related costs of water option trading determined by the model, and proves the superiority of fluctuating water price over stepped water price. Water option trading considering rainfall fully reflects the relationship between supply and demand in water market, and improves the scientificity of water option trading pricing in China.