Objective Computed tomography pulmonary angiography (CTPA) is used for the main diagnosis in acute pulmonary embolism (APE). Determining the thrombus location in the pulmonary vascular tree is also important for predicting disease severity. This study aimed to analyze the correlation of the thrombus location and the clot burden with the disease severity and the risk stratification in patients with APE. Methods The study included patients with APE diagnosed by CTPA who were admitted to the hospital between January 28, 2016, and July 1, 2019. Data collected were markers of severity in APE, including patient demographics, comorbidities, length of hospital stay, pulmonary embolism severity index (PESI) score, modified PESI score, Wells score, risk stratification according to the American Heart Association, systolic blood pressure (SBP), right ventricle diameter to left ventricle diameter ratio, pulmonary arterial pressure, brain natriuretic peptide, troponin, D-dimer, and plasma lactate levels, and vessel location of the thrombus, clot burden score, ratio of the pulmonary artery trunk diameter/aortic diameter, superior vena cava diameter (SVC) by CTPA, and survival. All parameters were analyzed in correlation with clot load and vessel location. Results Thrombus vascular location was found to be correlated with risk stratification and negatively correlated with SBP. Simplified Mastora score was correlated with risk stratification, SVC diameter, and D-dimer and negatively correlated with SBP. Occlusion of both the pulmonary artery trunk and any pulmonary artery with thrombus was associated with massive APE. Conclusion The level of the occluded vessel on CTPA may provide the ability to risk-stratify, and the clot burden score may be used for assessing both risk stratification and cardiac strain.