The diagnostic performance of magnetic resonance (MR) sequences for displaying different levels of pulmonary artery involvement in pulmonary embolism (PE) has rarely been reported but is essential for critically ill and emergency patients. The aim of the present study was to analyze the diagnostic accuracy of true fast imaging with steady-state precession (true FISP), MR pulmonary angiography (MRPA) and volume-interpolated body examination (VIBE) for PE detection in comparison to CT pulmonary angiography (CTPA), which is the reference standard. A total of 21 patients with confirmed deep venous thrombosis suspected of having PE were enrolled. Emboli were evaluated on per-patient and per-vessel bases. The evidence of PE on a per-vessel basis was classified into central, lobar and segmental levels, and 27 vessel segments per patient were analyzed for a total of 567 vessel segments in all patients. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated. Receiver operating characteristic curves were drawn to compare differences in sequences. A total of 158 pulmonary vessels were involved with emboli on CTPA, 58 of which were identified by true FISP, 63 by MRPA and 94 by VIBE. On per-patient and per-vessel bases, the sensitivity was 81.3 and 36.7%, respectively, for true FISP, 82.4 and 56.3%, respectively, for MRPA, and 94.4 and 68.1%, respectively, for VIBE; the specificity was 80.0 and 99.8%, respectively, for true FISP, 100 and 99.2%, respectively, for MRPA, and 100 and 99.2%, respectively, for VIBE. The respective PPV was 92.9 and 98.3% for true FISP, 100 and 95.5% for MRPA, 100 and 96.9% for VIBE. The NPV was 57.1 and 80.3%, respectively, for true FISP, 50.0 and 88.2%, respectively, for MRPA, and 75.0 and 89.8%, respectively, for VIBE. In conclusion, enhanced VIBE surpassed the other two sequences in revealing PE, particularly in segmental analysis, which is essential for emergency patients who have contraindications for receiving iodinated contrast and those who have concerns about the ionizing radiation.