Background Clinical and imaging manifestations are similar in pulmonary artery sarcomas (PAS) and thromboembolic diseases, especially central chronic pulmonary thromboembolism (CPTE). The feasibility of utilising clinical imaging tools such as computed tomography (CT) and magnetic resonance imaging (MRI) for differential diagnosis of PAS and CPTE has not been fully explored, especially MRI. Methods Patients with PAS (n = 18) and central CPTE (n = 20) treated at our hospital between January 2013 and September 2016 were identified retrospectively. Computed tomography and MRI findings of pulmonary artery (PA) filling defects including the location, the involvement of pulmonary artery, morphology, signal intensities and enhancement in MRI, calcification, sizes of right atrium and ventricle, inner diameters of the pulmonary artery trunk and branches, and mediastinal collateral circulation in both groups were examined, and differences were analysed by Fisher exact test and independent sample t-test. Results Compared to those of central CPTE, PAS lesions were in full shape or expansive growth (p < 0.001), and the proximal end of the tumours was often bulging or lobulated (p < 0.001). These lesions were aneurysm- or grape-like distally (p < 0.01) with inhomogeneous enhancement (p < 0.001). The MRI contrast enhancement pattern of PAS lesions were cloudy with inhomogeneous delayed enhancement and the time- density curves for some of the lesions increased gradually. Conclusion Computed tomographic and MR imaging manifestations may resemble PAS and central CPTE; however, some manifestations still have great value for the differential diagnosis of these two conditions, specifically the morphology and MRI enhancement patterns.