PURPOSE: With the evolving disease spectrum, chronic diseases have emerged as a primary burden and a leading cause of mortality. Due to the aging population and the nature of chronic illnesses, patients often suffer from multimorbidity. Predicting the likelihood of these patients developing specific diseases in the future based on their current health status and age factors is a crucial task in multimorbidity research. METHODS: We propose an algorithm, CE-GCN, which integrates age sequence and embeds Graph Convolutional Network (GCN) into Gated Recurrent Unit (GRU), utilizing the topological feature of network common neighbors to predict links in dynamic complex networks. First, we constructed a disease evolution network spanning from ages 45 to 90 years old using disease information from 3333 patients. Then, we introduced an innovative approach for link prediction aimed at uncovering relationships between various diseases. This method takes into account patients' age to construct the evolutionary structure of the disease network, thereby predicting the connections between chronic diseases. RESULTS: Results from experiments conducted on real networks indicate that our model surpasses others regarding both MRR and MAP. The proposed method accurately reveals associations between diseases and effectively captures future disease risks. CONCLUSION: Our model can serve as an objective and convenient computer-aided tool to identify hidden relationships between diseases in order to assist healthcare professionals in taking early disease interventions, which can substantially lower the costs associated with treating multimorbidity and enhance the quality of life for patients suffering from chronic conditions.