Presurgical evaluation is still challenging for MRI‐negative epilepsy patients. As non‐invasive modalities are the easiest acceptable and economic methods in determining the epileptogenic zone, we analyzed the localization value of common non‐invasive methods in MRI‐negative epilepsy patients. In this study, we included epilepsy patients undergoing presurgical evaluation with presurgical negative MRI. MRI post‐processing was performed using a Morphometric Analysis Program (MAP) on T1‐weighted volumetric MRI. The relationship between MAP, magnetoencephalography (MEG), scalp electroencephalogram (EEG), and seizure outcomes was analyzed to figure out the localization value of different non‐invasive methods. Eighty‐six patients were included in this study. Complete resection of the MAP‐positive regions or the MEG‐positive regions was positively associated with seizure freedom (p = 0.028 and 0.007, respectively). When an area is co‐localized by MAP and MEG, the resection of the area was significantly associated with seizure freedom (p = 0.006). However, neither the EEG lateralization nor the EEG localization showed statistical association with the surgical outcome (p = 0.683 and 0.505, respectively). In conclusion, scalp EEG had a limited role in presurgical localization and predicting seizure outcome, combining MAP and MEG results can significantly improve the localization of epileptogenic lesions and have a positive association with seizure‐free outcome.Plain Language SummaryDue to the lack of obvious structure abnormalities on neuroimaging examinations, the identification of epilepsy lesions in MRI‐negative epilepsy patients can be difficult. In this study, we intended to use non‐invasive examinations to explore the potential epileptic lesions in MRI‐negative epilepsy patients and to determine the results accuracy by comparing the neuroimaging results with the epilepsy surgery outcomes. A total of 86 epilepsy patients without obvious structure lesions on MRI were included, and we found that the combinations of different non‐invasive examinations and neuroimaging post‐processing methods are significantly associated with the seizure freedom results of epilepsy surgery.