In order to meet the new requirements of fault diagnosis response and intelligent degree in the current computer network, a fault detection of computer communication network based on an improved neural network algorithm is proposed. First, from the perspective of deep learning, based on the KDD99 data set, the network fault diagnosis method based on the convolutional neural network model is studied, and the data conversion operation of grayscale matrixed raw data is proposed. And experiments are carried out, the convolutional neural network structure is designed according to the scale of data features, a series of optimization studies including discarding learning, gradient optimization algorithm, and data enhancement based on this is carried out, and the establishment of the entire fault diagnosis model is completed. The experimental results show that, in the diagnostic model designed in this paper, the Tanh activation function is used in the first fully connected layer to achieve the best convergence speed. During the training process, it can start to converge after about 24 iterations, and the accuracy rate of the model training process can reach 98.1%, verifying the correctness and superiority of the algorithm and model.