The fluctuating asymmetry (FA) of fish otoliths can reflect the difference in the growth and development of fish in sea areas greatly affected by environmental pressure, thus enabling the assessment of different habitats. In this study, using 113 Collichthys lucidus samples collected from different functional areas (estuary area, aquaculture area, artificial reef area and natural area) in Haizhou Bay, the square coefficient of asymmetry variation (CV2a) of four characters (length, width, perimeter and area) of the left and right sagittal otoliths was calculated. The results showed that the CV2a value of otolith width was the lowest and that of otolith length was the highest. The CV2a value had no obvious regularity with increasing fish body length. In addition, the CV2a values of the four characteristics reached their lowest values in the artificial reef area, indicating that the construction of marine ranching dominated by artificial reefs may partly improve the aquatic environment in this functional area. We consider that the otolith FA of C. lucidus can be used as a characteristic of environmental stress between different areas/regions/habitats.