Background Numerous factors have been investigated on affecting the outcomes of primary hemifacial spasm (HFS) after microvascular decompression (MVD). It is well established that anatomical differences of the posterior cranial fossa (PCF) plays an important role in the occurrence of HFS. However, it is still not clear whether morphological characteristics of PCF affect the surgical outcomes of HFS after MVD. Our study aims to investigate the prognostic factors for surgical outcomes of MVD for primary HFS, with a particular focus on the morphological characteristics of PCF. Methods Between January 2014 and November 2017, a total of 152 HFS patients who underwent MVD treatment in our department were included in this study. The clinical data were retrospectively reviewed. The outcomes of MVD were classified into success and failure groups according to the short- and long-term postoperative responses. Particularly, we established an ellipsoid model for PCF. The related length (Y), width (X) and height (Z) of the PCF were measured and the volume of PCF was calculated employing a formula of pi/6XYZ. The relationship between PCF volume and surgical outcomes was statistically analysed. Results The severity of neurovascular compression (NVC) (p = 0.010), type of NVC (p = 0.001) and lateral spread response (LSR) (p < 0.0001) significantly influenced the long-term surgical outcomes of MVD for primary HFS. In particular, for the first time, we demonstrated that a flat-shaped PCF was associated with poor long-term outcome and postoperative recurrence. Conclusions Our current study suggests that mild NVC, small vessel compression, intraoperative LSR persistence and flat-shaped PCF are independent factors predicting poor prognosis of MVD for primary HFS.