Zebrafish is widely used in bone research, but there is a lack of methods to assess its bone development in vivo. The objective of this study was to monitor skull growth of zebrafish and investigate whether a correlation exists between the bone thickness and body length and age. The skull of zebrafish with different body lengths or ages were evaluated using optical coherence tomography (OCT) and histology. There was a significant normal linear correlation between these two methods (r=0.9988, P<0.05). Both OCT and histology showed that the skull thicknesses of older zebrafish were markedly higher than younger zebrafish (P<0.05), but no significant difference was found between zebrafish with the same age but different body lengths (P>0.05). This study demonstrated the age of zebrafish, not their body length can represent their developmental stages.OCT providing a powerful tool for noninvasive and nondestructive procedures in analyzing bone growth processes in long-time studies.