Epilepsy is one of the largest neurological diseases in the world, and juvenile myoclonic epilepsy (JME) usually occurs in adolescents, giving patients tremendous burdens during growth, which really needs the early diagnosis. Advanced diffusion magnetic resonance imaging (MRI) could detect the subtle changes of the white matter, which could be a non-invasive early diagnosis biomarker for JME. Transfer learning can solve the problem of insufficient clinical samples, which could avoid overfitting and achieve a better detection effect. However, there is almost no research to detect JME combined with diffusion MRI and transfer learning. In this study, two advanced diffusion MRI methods, high angle resolved diffusion imaging (HARDI) and neurite orientation dispersion and density imaging (NODDI), were used to generate the connectivity matrix which can describe tiny changes in white matter. And three advanced convolutional neural networks (CNN) based transfer learning were applied to detect JME. A total of 30 participants (15 JME patients and 15 normal controls) were analyzed. Among the three CNN models, Inception_resnet_v2 based transfer learning is better at detecting JME than Inception_v3 and Inception_v4, indicating that the "short cut" connection can improve the ability to detect JME. Inception_resnet_v2 achieved to detect JME with the accuracy of 75.2% and the AUC of 0.839. The results support that diffusion MRI and CNN based transfer learning have the potential to improve the automated detection of JME.