This paper proposes a comprehensive method for estimating thrombus formation factors in the left atrial appendage (LAA). First, using 3D CT (Computer Tomography) image data as input, classification of thrombus presence/absence is learned using 3D ResNet. Besides, 3D Grad-CAM is applied to the prediction results to visualize regions of interest in thrombus formation. Second, features are extracted based on the visualization of regions of interest. Using the extracted features and numerical data obtained from the hospital as input, a regression analysis is performed to predict the presence/absence of thrombus using LightGBM. Visualization of regions of interest using 3D ResNet and 3D Grad-CAM shows that the right inferior pulmonary vein and the LAA were particularly correlated with thrombus formation. Estimation of important factors for thrombus formation using LightGBM shows that the LAA ostium area has the greatest influence on thrombus formation.Clinical Relevance-This paper shows the factors that contribute to thrombus formation in the LAA from the viewpoint of three-dimensional structure. In addition, the features considered important in thrombus formation were identified by comparing a variety of features.