Objective To investigate the application of Magnetoencephalograph (MEG), Wada test combined with neuronavigation in the surgical treatment of frontal and temporal epilepsy caused by focal cortical dysplasia (FCD ). Methods The epileptogenic focus and IQ, memory and language examination were performed in 34 patients with frontal and temporal epilepsy caused by FCD. MEG and Wada test were conducted to determine the language and memory advantage hemisphere, and to clarify the scope and memory function of language function areas. Operation was guided by the Medtronic stealhealth 7 surgical navigation system (USA) to remove the FCD and protect nerve function. IQ, memory and language examination were measured 1 year after operation, and the difference was observed before and after operation. The postoperative follow-up was 23 ~ 46 months, curative effect of epilepsy was determined according to the international anti-epilepsy union Engel’s standard. Results Thirty-four patients with epilepsy (21 temporal lobe epilepsy and 13 frontal lobe epilepsy) were included in this study. The examination process of MEG and Wada test was smooth. MEG can accurately locate the position of language function area. Twenty-eight patients’ dominant hemisphere of language was on the left and 6 was on the right side. Wada test can evaluate the patient’s memory function. Twenty-three patients’ dominant hemisphere of memory was located on the left, 8 on the right and 3 on the bilateral hemisphere. Compared with the dominant hemisphere and nondominant hemisphere, the memory score was significantly different (P<0.05). Statistics showed that the verbal IQ and total IQ increased (P<0.05)1 year after operation, but there was no significant change in memory IQ and Performance IQ (P>0.05). FCD patients recovered well without language, memory and limb impairment. The curative effect of epilepsy: 15 cases of Engel’sⅠgrade, 14 cases of Engel’sⅡgrade and 5 cases of Engel’s Ⅲ grade. Conclusion MEG, Wada test combined with neuronavigation was of important value in locating and guiding the surgical resection of FCD in patients with refractory frontal and temporal epilepsy, protecting cortical function, avoiding severe postoperative complications, and improving the therapeutic effect of epilepsy.