Interaction between childhood trauma and genetic factors influences the pathophysiology of posttraumatic stress disorder (PTSD). This study examined the interaction effect of childhood trauma and brain-derived neurotrophic factor (BDNF) Val66Met polymorphism on PTSD symptoms and brain cortical thickness. A total of 216 participants (133 healthy volunteers and 83 PTSD patients) were recruited. T1-weighted structural magnetic resonance imaging, BDNF rs6265 genotyping through blood sampling, and clinical assessments including the childhood trauma questionnaire (CTQ) and posttraumatic stress disorder Checklist (PCL) were performed. A moderated regression analysis, two-way multivariate analysis of covariance, and correlation analysis were conducted. An interaction between the CTQ and the BDNF polymorphism significantly influenced PTSD symptom severity. In fact, people with rs6265 Val/Val genotype and higher CTQ scores showed higher PCL scores. Additionally, this interaction was significant on both left fusiform and transverse temporal gyri thickness. Furthermore, the thickness of both brain regions was significantly correlated with psychological symptoms including depression, anxiety, rumination, and cognitive emotion regulation methods; yet this was mainly observed in people with the Val/Val genotype. The interaction between childhood trauma and BDNF polymorphism significantly influences both PTSD symptoms and cortical thickness and the Val/Val genotype may increase the risk in Korean population.