Aiming at the dynamic supply chain partners in the cloud computing environment, this paper puts forward a supply chain partner selection based on optimizing neural network in cloud computing. Firstly, evaluation system of supply chain partner is constructed in cloud computing environment, and every index weight of is calculating by analytic hierarchy process, and then neural network is used to evaluate enterprise based on training samples, while genetic algorithm is used to optimize the parameters of neural network and to establish evaluation model of enterprise, finally, the simulation experiment is used to test the performance. The results show that the proposed model can accurately describe the dynamic change of supply chain partners. It also can comprehensive evaluate supply chain partners under the cloud computing environment.