Objective To explore the value of multi-slice spiral CT (MSCT) combined with magnetic resonance imaging (MRI) in the diagnosis of pulmonary embolism. Methods A total of Sixty-six patients with pulmonary embolism diagnosed by imaging examination in the hospital from February 2015 to August 2017 were selected as the study subjects. All patients underwent MSCT and MRI scans, and digital subtraction angiography (DSA) was performed for confirmed diagnosis. Images of MSCT and MRI were analyzed by two imaging physicians. The effects of MSCT, MRI and MSCT combined with MRI in diagnosis of pulmonary embolism were compared. Results MSCT showed 145 involved pulmonary arteries while MRI showed 137 pulmonary arteries in 66 patients. MSCT combined with MRI showed 154 pulmonary arteries. The direct signs included different degrees of filling defects in pulmonary arteries, while indirect signs included mosaic sign, pulmonary hypertension, pleural effusion and cerebral infarction, etc.. With the diagnostic results of DSA as the golden standard, the diagnostic sensitivities of MSCT, MRI and MSCT combined with MRI were 92.94%, 87.82% and 98.71%, respectively (P<0.05). Conclusion MSCT combined with MRI is significantly better than single MSCT or MRT in the diagnosis of pulmonary embolism. It can be used as a reference for the diagnosis of pulmonary embolism.