Accurate calculation of lung cancer dose using the Monte Carlo (MC) algorithm in CyberKnife (CK) is essential for precise planning. We aim to employ deep learning to directly predict the 3D dose distribution calculated by the MC algorithm, enabling rapid and accurate automatic planning. However, most current methods solely focus on conventional intensity-modulated radiation therapy and assume a consistent beam configuration across all patients. This study seeks to develop a more versatile model incorporating variable beam configurations of CK and considering the patient's anatomy.This study proposed that the AB (anatomy and beam) model be compared with the control Mask (only anatomy) model. These models are based on a 3D U-Net network to investigate the impact of CK beam encoding information on dose prediction. The study collected 86 lung cancer patients who received CK's built-in MC algorithm plans using different beam configurations for training/validation (66 cases) and testing (20 cases). We compared the gamma passing rate, dose difference maps, and relevant dose-volume metrics to evaluate the model's performance. In addition, the Dice similarity coefficients (DSCs) were calculated to assess the spatial correspondence of isodose volumes.The AB model demonstrated superior performance compared to the Mask model, particularly in the trajectory dose of the beam. The DSCs of the AB model were 20-40% higher than that of the Mask model in some dose regions. We achieved approximately 99% for the PTV and generally more than 95% for the organs at risk (OARs) referred to the clinical planning dose in the gamma passing rates (3 mm/3%). Relative to the Mask model, the AB model exhibited more than 90% improvement in small voxels (p < 0.001). The AB model matched well with the clinical plan's dose-volume histograms, and the average dose error for all organs was 1.65 ± 0.69%.Our proposed new model signifies a crucial advancement in predicting CK 3D dose distributions for clinical applications. It enables planners to rapidly and precisely predict MC doses for lung cancer based on patient-specific beam configurations and optimize the CK treatment process.© 2024. The Author(s).