At present, the traditional model of PE in PSS (PSS)has seriously affected the quality of PE teaching in PSS and the perception of PE among primary and secondary school students. Because of the urgent need for innovation in PE in PSS, this study proposes the LSTM model to achieve an accurate prediction of the innovation direction of PE in PSS. Based on the LSTM model, the user behavior is classified by extracting the important features of the innovation direction. Expression to achieve accurate prediction of the future development direction of PE. Using the data confusion matrix to estimate the prediction accuracy of the LSTM model, the four evaluation indicators of Accuracy, Precision, F1, and AUC are 0.0532~0.2323 higher than the baseline model. The prediction results of PE teaching innovation in PSS from three aspects of teaching thought, teaching content, teaching objectives and essence are output, which has obvious guiding significance for the overall optimization of PE classrooms in PSS. This result shows that the LSTM prediction model has important practical value.