Aiming the problems that the clinical data of different patients is difficult for reasonable representation and the time interval between medical events is different, which lead to the difficulty of clinical prediction, a clinical prediction model based on the long short-term memory (LSTM) network optimized by fruit fly optimization algorithm in health time series data is proposed. First, FastText method is used to represent the interpretable vector of medical events, which can extract the concept relationship rich in medical information more effectively. Then, considering the strong dependence of clinical data on time stamp, LSTM network is used to model clinical events for better extraction of long-term and short-term information, so as to improve the prediction performance of the model. Finally, the fruit fly optimization algorithm is used to find the optimal super parameters of LSTM network, which can improve the training efficiency and prediction precision of the network. Experimental results on MIMIC datasets show that the prediction precision, Recall@k and MAP@k of the proposed model are better than those of other models. The validity of the model is proved.