Exercise has long been known to improve cardiovascular health, energy metabolism, and well-being. However, myocardial cell responses to exercise are complex and multifaceted due to their molecular pathways. To understand cardiac physiology and path physiology, one must understand these pathways, including energy autophagy. In recent years, deep learning techniques, IoT devices, and cloud computing infrastructure have enabled real-time, large-scale biological data analysis. The objective of this work is to extract and analyze autophagy properties in exercise-induced cardiac cells in a cloud-IoT context using deep learning, more especially an autoencoder. The Shanghai University of Sport Ethics Committee for Science Research gave its approval for the data collection, which involved 150 male Sprague–Dawley (SD) rats that were eight weeks old and in good health. The [Formula: see text]-score normalization method was used to standardize the data. Fractal optimization methods could be applied to these algorithms. For example, fractal-inspired optimization techniques might be used to analyze deep learning with Autoencoder, the autography energy of exercise myocardial cells within a cloud-IoT. To capture the intricate myocardial energy autophagy during exercise, we introduced the DMO-GCNN-Autoencoder, a Dwarf Mongoose Optimized Graph Convolutional Neural Network. The results showed that the proposed network’s performance matches that of the existing methods.