With the rapid development of Internet medical information technology, a large amount of medical data appeared on the Internet, however, how to extract effective information from the massive and complex medical data to provide professional medical services and suggestions to users has become a hot spot for this research. The recommendation system can effectively solve the problem of accurate matching of complex medical data resources; however, the cold start, data sparsity and user interest migration of the system in the complex data environment have a large impact on the recommendation effect; therefore, this paper proposes a weighted neural matrix decomposition improved health management recommendation scheme incorporating deep learning techniques. The scheme first uses an implicit feedback method to improve the prediction scores and improve the linear model performance of the matrix decomposition algorithm to form a weighted neural matrix decomposition health management recommendation algorithm. Second, the improved method and deep neural network are fused to improve the performance of the nonlinear model part of the algorithm by using the structural properties of the neural network. Finally, this paper’s method is compared with the mainstream six recommendation algorithms on four publicly available real datasets. The experimental results show that the root mean square error (RMSE) of the WENMF algorithm is smaller than that of the comparison algorithm on all four datasets, and the convergence speed is faster. The hit rate (HR) and normalized discounted cumulative gain (NDCG) of the WENMF algorithm are higher than those of the comparison algorithm on all four datasets, and the maximum difference is 0.04. Therefore, the recommendation accuracy and ranking quality of the WENMF algorithm in the recommendation system are verified, and the cold start and data sparsity problems of the recommendation system are effectively alleviated.