Objective To investigate the type of offending vessels, the position of nerve compression by vessels, and the association between the degree of nerve compression and the volume of the trigeminal nerve in patients with primary trigeminal neuralgia (PTN).Methods A retrospective analysis was performed for the clinical data of 65 patients with PTN who underwent microvascular decompression (MVD) in our hospital (case group), and 35 healthy individuals who underwent physical examination in our hospital during the same period of time were enrolled as control group. Magnetic resonance imaging (MRI) was performed to measure the cisternal volume and the coronal sectional area of the bilateral trigeminal nerve, which was then compared between the two groups. The cisternal volume and the coronal sectional area of the bilateral trigeminal nerves were compared between the patients with different types of offending vessels or locations and degrees of nerve compression.Results For the case group, the volume and the coronal sectional area of the trigeminal nerve of the symptomatic side were significantly lower than those of the non-symptomatic side (P<0.01), and compared with the control group, the case group had significantly lower volume and coronal sectional area of the trigeminal nerve of the symptomatic side (P<0.01), while there were no significant differences in the volume and the coronal sectional area of the trigeminal nerve of the non-symptomatic side between the two groups (P>0.05). Compared with the venous compression group, the arterial compression group had significant increases in the cisternal volume and the coronal sectional area of the bilateral trigeminal nerves (P<0.05). There were significant differences in the cisternal volume and the coronal sectional area of the bilateral trigeminal nerves between the patients with different locations of nerve compression (P<0.05). Compared with the grade I compression group, the grade II-III groups had significant increases in the cisternal volume and the coronal sectional area of the bilateral trigeminal nerves (P<0.05); compared with the grade II compression group, the grade III compression group had significant increases in the cisternal volume and the coronal sectional area of the bilateral trigeminal nerves (P<0.05).Conclusions The atrophy of the cisternal segment of the trigeminal nerve is closely associated with the pathogenesis of PTN, and the degree of the atrophy of the trigeminal nerve is different between patients with different types of offending vessels and positions and degrees of nerve compression, suggesting that the atrophy of the cisternal segment of the trigeminal nerve may be of great value in the diagnosis of PTN.