In drug discovery, the search for new and effective medications is often hindered by concerns about toxicity. Numerous promising molecules fail to pass the later phases of drug development due to strict toxicity assessments. This challenge significantly increases the cost, time, and human effort needed to discover new therapeutic molecules. Additionally, a considerable number of drugs already on the market have been withdrawn or re-evaluated because of their unwanted side effects. Among the various types of toxicity, drug-induced heart damage is a severe adverse effect commonly associated with several medications, especially those used in cancer treatments. Although a number of computational approaches have been proposed to identify the cardiotoxicity of molecules, the performance and interpretability of the existing approaches are limited. In our study, we proposed a more effective computational framework to predict the cardiotoxicity of molecules using an attention-based graph neural network. Experimental results indicated that the proposed framework outperformed the other methods. The stability of the model was also confirmed by our experiments. To assist researchers in evaluating the cardiotoxicity of molecules, we have developed an easy-to-use online web server that incorporates our model.