This study aims to explore the relationship between neuropathologic and the post-surgical prognosis of focal cortical dysplasia (FCD) typed-Ⅲ-related medically refractory epilepsy. A total of 266 patients with FCD typed-Ⅲ-related medically refractory epilepsy were retrospectively studied. Presurgical clinical data, type of surgery, and postsurgical seizure outcome were analyzed. The minimum post-surgical follow-up was 1 year. A total of 266 patients of FCD type Ⅲ were included in this study and the median follow-up time was 30 months (range, 12~48 months). Age at onset ranged from 1.0 years to 58.0 years, with a median age of 12.5 years. The number of patients under 12 years old was 133 (50%) in patients with FCD type Ⅲ. A history of febrile seizures was present in 42 (15.8%) cases. In the entire postoperative period, 179 (67.3%) patients were seizure-free. Factors with p < 0.15 in univariate analysis, such as age of onset of epilepsy (p = 0.145), duration of epilepsy (p = 0.004), febrile seizures (p = 0.150), being MRI-negative (p = 0.056), seizure type (p = 0.145) and incomplete resection, were included in multivariate analysis. Multivariate analyses revealed that MRI-negative findings of FCD (OR 0.34, 95% CI 0.45–0.81, p = 0.015) and incomplete resection (OR 0.12, 95% CI 0.05–0.29, p < 0.001) are independent predictors of unfavorable seizure outcomes. MRI-negative finding of FCD lesions and incomplete resection were the most important predictive factors for poor seizure outcome in patients with FCD type Ⅲ.