Objective To investigate the clinical diagnostic value of CT and MRI in early lacunar infarction (LAC). Methods A total of 250 LAC patients treated in our hospital from January 2015 to June 2017 were given CT and MRI examination. Results A total of 451 lesions were found in 250 patients through CT examination demonstrated as hypodensity or isodensity, while a total of 1048 lesions were found through MRI detection. The detection rate in MRI group was significantly higher than that in CT group (P<0.05). The lesion diameter of CT group was 5-18mm, the mean diameter was (10.59±1.58) mm, including 6 lesions size ≤ 5mm, 184 lesions size between 5mm to 10mmm and 261 lesions size ≥10mm. The lesion diameter of MRI group was 2-18mm, the mean diameter was (4.59±1.48) mm, including 489 lesions size ≤ 5mm, 290 lesions size between 5mm to 10mmm and 269 lesions size ≥10mm. The≤ 5mm lesions detection rate in MRI group was significantly higher than that in CT group (P<0.05). CT results showed that the incidence of new lesions in basal ganglia, asymptomatic infarction, enlarged perivascular space and intracranial atheromatous white matter lesions in LAC patients were significantly higher than those in severe patients (P<0.05). While the MRI results showed that the incidence of above disease in LAC patients were higher than that in the mild patients (P<0.05). The average detection time and cost of CT group were significantly lower than those of MRI group (P<0.05). Conclusion LAC can be detected by both CT and MRI examinations. The MRI has the advantages of higher small lesions detection rate and determining the degree of white matter disease.