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Objective Intracranial aneurysm (IAN) is a class of cerebrovascular diseases with a serious threat to patients, and an accurate diagnosis of IAN is very important for both selection of the appropriate therapy and prediction of the prognosis. This study aimed to evaluate the diagnostic values of zero-echo-time magnetic resonance angiography (ZTE-MRA) and time-of-flight magnetic resonance angiography (TOF-MRA) in patients with IAN. Methods Digital subtraction angiography, ZTE-MRA, and TOF-MRA were performed in 18 patients diagnosed with IAN. The images of ZTE-MRA and TOF-MRA were compared for image quality, qualitative diagnosis, detailed diagnosis, number of thrombi, and residual aneurysm lumen, with digital subtraction angiography as the reference. Results Zero-echo-time MRA and TOF-MRA did not show a significant difference in image quality or detailed information (including aneurysm size, growth direction, and angle with the aneurysm-carrying vessel) (P > 0.05). However, ZTE-MRA showed advantages over TOF-MRA in terms of qualitative diagnosis (sensitivity and specificity), intra-aneurismal thrombus detection, and residual aneurysm lumen detection after embolization (P < 0.05). Conclusions Compared with TOF-MRA, ZTE-MRA showed greater diagnostic value for IAN patients in terms of qualitative diagnosis, as well as the detection of intra-aneurysm thrombi and residual aneurysm lumen after embolization.