To diagnose pulmonary embolism (PE) with dual source CT (DSCT) dual energy perfusion imaging, and to explore the relationships of the positions and morphology of the pulmonary emboli with dual energy perfusion imaging. Methods DSCT dual energy perfusion imaging was performed in 120 cases suspected as PE. The pulmonary embolus position and types were analyzed and compared with the types of perfusion defects. The coincidence of pulmonary artery enhanced scanning in mediastinum window and pulmonary perfusion imaging in diagnoses of PE and PE pulmonary perfusion changes were analyzed. Results Firstly, a series of analysis of pulmonary embolus position revealed that the embolism rate of right pulmonary artery was higher than that of left pulmonary artery, the embolism rates of lobar arteries were higher than those of the left and right pulmonary trunks, the embolism rates of the pulmonary arteries in the lower lobes were higher than those of the pulmonary arteries in the upper lobes. The morphological assessment of pulmonary emboli showed that central type and complete occlusion type were in the majority,followed by mural type, and irregular type and saddle type were in the minority. Secondly, among the types of pulmonary trunk emboli, the complete occlusion type frequently occurred in the whole lung or lobar perfusion defects, however, the central or mural type more often occurred in pulmonary lobar or segmental perfusion defects. If PE occurred in pulmonary lobe or segment, the complete occlusion type mostly appeared in pulmonary lobar or segmental perfusion defects, while the mural type or center type largely appeared in pulmonary segmental or subsegmental perfusion defects or the lungs without perfusion defect. If PE occurred in the subsegments of the lungs, there was usually subsegmental perfusion defect or no perfusion defect. Thirdly, the pulmonary enhanced scanning in mediastinum window and pulmonary perfusion imaging were in good coincidence for diagnosis of pulmonary embolism, but in bad coincidence for diagnosis of PE pulmonary perfusion changes. Conclusions Pulmonary perfusion imaging is related with the locations and shapes of pulmonary emboli. DSCT dual energy pulmonary perfusion imaging can be used to diagnose pulmonary embolism.