Medication recommendation based on Electronic Health Records (EHRs) is a significant research direction in the field of intelligent medicine, which aims to recommend personalized medication combinations for patients based on their historical and current physical conditions. However, since the structural and temporal characteristics of medical records are affected by many uncertain factors, there are many limitations in medication recommendation methods based on EHRs. Specifically, most existing works either fail to adequately assess the structural correlation and temporal dependency among various medical entities or ignore existing knowledge of Drug–Drug Interactions (DDI), which could lead to adverse outcomes. These factors contribute to poor recommendation quality. Therefore, we propose a medical ontology tree model combined with the Graph Attention Networks (GAT) for medication recommendations. First, the class hierarchy extracted from the medical ontology and the GAT model is used to learn the ICD-9 codes of diagnoses and procedures, which enriches the semantic representation of medical entities. Secondly, Gate Recurrent Units (GRU) are used to learn the temporal characteristics of medical entities. Finally, memory bank, dynamic memory and DDI graph are used to optimize the hidden layer results, which improve the accuracy of the model. Experimental results show that the proposed model is superior to the previous methods in all evaluation indicators, and the recommended results have a lower DDI rate.