BACKGROUND: Pulmonary embolism (PE) is a common and potentially fatal condition. Timely and accurate risk assessment in patients with acute deep vein thrombosis (DVT) is crucial. This study aims to develop a deep learning-based, precise, and efficient PE risk prediction model (PE-Mind) to overcome the limitations of current clinical tools and provide a more targeted risk evaluation solution. METHODS: We analyzed clinical data from patients by first simplifying and organizing the collected features. From these, 37 key clinical features were selected based on their importance. These features were categorized and analyzed to identify potential relationships. Our prediction model uses a convolutional neural network (CNN), enhanced with three custom-designed modules for better performance. To validate its effectiveness, we compared this model with five commonly used prediction models. RESULTS: PE-Mind demonstrated the highest accuracy and reliability, achieving 0.7826 accuracy and an area under the receiver operating characteristic curve of 0.8641 on the prospective test set, surpassing other models. Based on this, we have also developed a Web server, PulmoRiskAI, for real-time clinician operation. CONCLUSION: The PE-Mind model improves prediction accuracy and reliability for assessing PE risk in acute DVT patients. Its convolutional architecture and residual modules substantially enhance predictive performance.