Although phase separation is a ubiquitous phenomenon, the interactions between multiple components make it difficult to accurately model and predict. In recent years, machine learning has been widely used in physics simulations. Here, we present a physical information-enhanced graph neural network (PIENet) to simulate and predict the evolution of phase separation. The accuracy of our model in predicting particle positions is improved by 40.3% and 51.77% compared with CNN and SVM respectively. Moreover, we design an order parameter based on local density to measure the evolution of phase separation and analyze the systematic changes with different repulsion coefficients and different Schmidt numbers. The results demonstrate that our model can achieve long-term accurate predictions of order parameters without requiring complex handcrafted features. These results prove that graph neural networks can become new tools and methods for predicting the structure and properties of complex physical systems.