Objective To analyze and compared the imaging findings and diagnostic values of Computed tomography (CT) and magnetic resonance imaging (MRI) in 85 patients with lacunar infarction (LI). Methods The clinical data of 85 LI patients treated with CT and MRI examinations at the same time in our hospital were analyzed retrospectively. The differences in the number, location and size of lesions detected by the two methods were compared. Results Among 85 LI patients, 751 lesions were detected by MRI and 149 lesions by CT, and the number of detected lesions by MRI was 5.04 times than that by CT, and the number of multiple lesions detected by MRI was significantly higher than that by CT (P<0.05). Detected lesions by MRI were mainly in frontal lobe, basal ganglia and parietal lobe while lesions detected by CT were mainly in internal capsule, basal ganglia and parietal lobe. The detection rates of frontal lobe, thalamus and cerebellum lesions by MRI were significantly higher than those by CT (P<0.05) while the detection rate of internal capsule lesions was lower than that by CT (P<0.05). However, there was no significant difference in the detection rates of basal ganglia, parietal lobe and brainstem lesions by the two methods (P>0.05). The detected lesions by MRI and CT were mainly with diameter≤ 5mm, accounting for 76.30% and 56.38% respectively. The detection rate of lesions diameter≤5 mm by MRI was significantly higher than that by CT (P <0.05) while the detection rate of lesions diameter> 5mm was lower than that by CT (P<0.05). Conclusion Both CT and MRI can be used for the diagnosis of LI, but MRI can detect more lesions, and can detect lesions more clearly. The accurate diagnosis of LI is more favorable.