Abstract: Objective To explore the effect of application of multimodal neural navigation technology with integration of MRI and CT images in skull base microsurgery. Methods Clinical data about 14 patients with skull base tumors admitted to our hospital from January 2013 to April 2014 were retrospectively analyzed. All patients had undergone microsurgery with the guidance of multimodal neural navigation technology with integration of MRI and CT images. The extent of resection of tumors and pre- and post-operative neural functional changes were evaluated. Results Of the 14 patients, near-total resection was achieved in 8 patients while sub-total resection was achieved in 6 patients. Three weeks after surgery, neurological function was improved or kept no change in 12 cases; 2 cases experienced neurological function decline, however the Karnofsky Performance Scale (KPS) score of these 2 patients were higher than 60, which suggested that the patients had the ability of self-care. Conclusion Multimodal neural navigation technology with integration of MRI and CT images provides comprehensive navigation information, which is helpful to maximize the resection of tumors and benefit for the safety of skull base microsurgery.