In the current research, cluster analysis has become a very good way to obtain biological information by analyzing the brain gene expression data. In recent years, many experts have used improved traditional clustering algorithm and a new clustering algorithm to mine brain gene expression data. First, the random Forest method is used to preprocess high-dimensional and high-complexity brain gene expression data. Then, a clustering model based on deep learning is proposed, and a clustering algorithm is implemented by using deep belief network (DBN) and fuzzy c-means algorithm (FCM). This model makes full use of the generality of unsupervised learning of deep learning and clustering technology, combines the advantages of deep learning with clustering, and makes clustering effect better and more convenient for clustering high-dimensional data. INDEX TERMS Deep belief network, fuzzy c-means algorithm, unsupervised learning, brain gene data clustering.