indexes is set up. The basic principle of the neural network is analyzed and then the BP neural network and linear neural network models are constructed and the output error function of the neural networks is introduced. The Matlab software is applied to set the parameters and calculate the neural networks. By computing a real-world example, the evaluation results of the scientific research projects are obtained and the results of the BP neural network, linear neural network and linear regression forecasting are compared. The analysis shows that the BP neural network has higher efficiency than the linear neural network and linear regression forecasting in the evaluation of the scientific research projects problem. The method proposed in this paper is an effective method to evaluate the scientific research projects.