Morphological traits measurement still plays a key role in description, identification, classification and phylogenetics of species. However, the traditional morphological measurement method is inefficient and often destructive to the studied organism. In this study, we propose and test an X‐ray‐based technique for non‐destructive morphological studies of fish. We use this approach to attempt to discriminate four species from the genus Megalobrama on the basis of their morphometric and meristic traits. The results showed that there were significant differences (p < 0.05) in the morphological traits among the four species, and the meristic traits were more stable than the morphometric traits. The result of principal component analysis indicated that morphometric characters of Megalobrama hoffmanni were significantly different from the other three species. Megalobrama pellegrini was used as a model to compare and evaluate the accuracy of the two methods (X‐ray and traditional manual), and the results revealed that except for the undifferentiated traits, most of the morphometric traits detected by the traditional manual method were significantly higher than that detected by the X‐ray photography. Also, many standard deviation values produced by the X‐ray photographic method were smaller. Therefore, X‐ray photography is a suitable method for non‐destructive and accurate detection of morphological parameters in the genus Megalobrama.