Intertidal mud crab (Macrophthalmus japonicus) is an organism with a hard chitinous exoskeleton and has function for an osmotic control in response to the salinity gradient of seawater. Crustacean exoskeletons change in their natural state in response to environmental factors, such as changes in the pH and water temperature, and the presence of pollutant substances and pathogen infection. In this study, the ecotoxicological effects of irgarol exposure and heavy metal distribution were presented by analyzing the surface roughness of the crab exoskeleton. The exoskeleton surface roughness and variation reduced in M. japonicus exposed to irgarol. In addition, it was confirmed that the surface roughness and variation were changed in the field M. japonicus crab according to the distribution of toxic heavy metals(Cd, Pb, Hg) in marine sediments. This change in the surface roughness of the exoskeleton represents a new end-point of the biological response of the crab according to external environmental stressors. This suggests that it may affect the functional aspects of exoskeleton protection, support, and transport. This approach can be utilized as a useful method for monitoring the aquatic environment as an integrated technology of mechanical engineering and biology.