Advanced Persistent Threats (APTs) have significantly impacted organizations over an extended period with their coordinated and sophisticated cyberattacks. Unlike signature-based tools such as antivirus and firewalls that can detect and block other types of malware, APTs exploit zero-day vulnerabilities to generate new variants of undetectable malware. Additionally, APT adversaries engage in complex relationships and interactions within network entities, necessitating the learning of interactions in network traffic flows, such as hosts, users, or IP addresses, for effective detection. However, traditional deep neural networks often fail to capture the inherent graph structure and overlook crucial contextual information in network traffic flows. To address these issues, this research models APTs as heterogeneous graphs, capturing the diverse features and complex interactions in network flows. Consequently, a hetero-geneous graph transformer (HGT) model is used to accurately distinguish between benign and malicious network connections. Experiment results reveal that the HGT model achieves better performance, with 100 \% accuracy and accelerated learning time, outperferming homogeneous graph neural network models.