In order to protect the environment and reduce energy consumption, new energy vehicles have begun to be vigorously promoted in various countries. In recent years, the rise of intelligent technology has had a great impact on the supply chain of new energy vehicles, which, coupled with the complexity of the supply chain itself, puts it at great risk. Therefore, it is quite indispensable to evaluate the risk of the new energy vehicle supply chain. This paper assesses the risks faced by China’s new energy vehicle supply chain in this period of technological transformation. First of all, this paper establishes an evaluation criteria system of 16 sub-criterion related to three dimensions: the market risk, operational risk, and the environmental risk. Then, variable weight theory is proposed to modify the constant weight obtained by the fuzzy analytic hierarchy process (FAHP). Finally, a risk assessment of China’s new energy vehicle supply chain is carried out by combining the variable weight and the cloud model. This method can effectively explain the randomness of matters, and avoid the influence of value abnormality on the criteria system. The results show that China’s new energy vehicle supply chain is at a high level. Through the identification of risk factors, mainly referring to the low clustering risk, technical level risk and information transparency risk, this paper can provide a risk prevention reference for corresponding enterprises.