Zebrafish serves as a valuable model for studying tissue regeneration due to their comprehensive regenerative abilities, particularly in bone tissue. In this study, a Mueller matrix optical coherence tomography (OCT) system was applied to monitor the regenerative processes of zebrafish caudal fins in vivo. The analysis focused on evaluating the thickness of the caudal fin tip and the distribution of internal bone tissue during the regenerative process. Subsequently, the effect of ectoine solution on the regeneration process was observed and discussed. Our findings revealed that the caudal fin blastema did not exhibit phase-induced polarization characteristics in the Mueller matrix OCT images. Statistical analyses indicated that the caudal fins did not fully regenerate to their original state within 21 days. Furthermore, the results suggested that ectoine solution could enhance tissue regeneration. This approach provides a method for quantifying zebrafish caudal fin regeneration and advances observation techniques for biomedical and clinical applications.