Objective To analyze and compare the application value of multi-slice spiral CT (MSCT) and magnetic resonance imaging (MRI) in the diagnosis of primary brain tumors. Methods 68 patients with primary brain tumors who were treated in our hospital from May 2016 to May 2018 were included in the study. All patients were admitted to the hospital by MSCT and MRI and other related imaging examination. Gender, age, disease status and related imaging data of all patients were collected. The diagnostic value of different examination for primary brain tumors was analyzed. Results The diagnose coincidence rate of MRI examination for brain tumor detection was 95.59%, which was significantly higher than that of MSCT examination that was 82.35% (χ2=6.069, P=0.014);In the MSCT examination, astroglioma was mass, mixed and high-density lesion, and a slightly lower density lesion was seen; meningioma mainly showed highdensity nodules; Higher density lesions were seen in ependymal tumors; flat scan of medulloblastomas showed a lower density of round tumors. In the MRI examination, astroglioma mainly showed elliptical lesions and is unevenly flower-ringed and displayed the nodosity enhancement. Meningiomas showed similar circular nodules and showed obvious signs of enhancement; Visible signal of the ependymal tumor was high, and the tumor T2 in the fourth ventricle was abnormal; There was no significant change in medulloblastoma scan, but it was enhanced after injection angiography. Conclusion Compared with MSCT, MRI has a significantly higher diagnose coincidence rate for brain tumors, and can show the pathological features better of tumors to provide a more powerful reference for clinical treatment.