We developed a real-time screening system using optical coherence tomography (OCT) to distinguish the fruitful melon seeds efficiently. Cross-section images of melon seeds infected with Cucumber green mottle mosaic virus (CGMMV) showed an additional layer that did not appear in normal seeds. Additional layer appeared under $100{sim}300{mu}m$ from the surface of the seed. OCT can visualize the micro-structural and morphological changes of the internal seed structure. Real-time OCT seed screening system provided the real-time, non-destructive, cross-section image and quantitative information such as A-scan analysis of selected region in the cross-section image. We can distinguish the viral infection seeds while monitoring the averaged A-scan analysis graph in real-time by considering the second peak value of the graph which refers to the layer that occurred owing to the virus. Real-time OCT seed screening system could assist to distinguish the disease caused by CGMMV.