Drosophila melanogaster has become an invertebrate genetic model for studies of genes-related diseases and developmental biology. Neurodegenerative diseases such Alzheimer and Parkinson's diseases are health problem and get worse with age. However, the causes and progress of neurodegenerative diseases are still poorly understood. The compound eye of Drosophila demonstrates a heterologous system to investigate neurodegenerative diseases. In this study, we propose to use optical coherence tomography (OCT) for the study of protein-related degeneration of Drosophila eyes. With OCT, the bristles of Drosophila eye can be identified and different mutant Drosophila were scanned with OCT for investigation of progress of protein-related degeneration. From the results, it can be noted that OCT could be a powerful and noninvasive inspection tool for protein-related degenerative diseases.