Purpose: To investigate the different clinical and cytogenetic features of skull base meningiomas (SBMs) and non-SBMs (NSBMs).Methods: We conducted a retrospective study on a series of 316 patients with primary intracranial meningiomas. The t-test and the Chi-square test were used to analyze the differences between 194 SBMs and 122 NSBMs. The Cox analysis was used to determine prognostic factors for tumor recurrence.Results: Compared with NSBMs, on average, the age of patients with SBMs was about 2.88 years younger (p = 0.024); the duration of operation of SBMs was 2.73 h longer (p < 0.001); the duration of hospital stays of patients with SBMs was about 6.76 days longer (p < 0.001); the tumor volume was 7.69 cm3 smaller (p = 0.025); the intraoperative blood loss was 147.61ml more (p = 0.039); the total cost of SBMs was 1.39 times more (p < 0.001); the preoperative KPS, postoperative KPS, and follow-up KPS of patients with SBMs were all respectively lower (p < 0.001); Gross total resection was less achieved (p < 0.001). SBMs (average of 20.80 per sample) had a smaller total number of copy number variations (CNVs) than NSBMs (29.98 per sample) (p = 0.009). Extremely large CNVs (> 5 Mb) were more likely to present in NSBMs (p < 0.001). Cox analysis showed that subtotal resection (p = 0.002) and the total number of CNVs (p = 0.015) were independent risk factors for tumor recurrence.Conclusions: The clinical and cytogenetic features of SBMs were different from NSBMs. Moreover, the degree of resection and the total number of whole-genome CNVs were independent prognostic factors for tumor recurrence.