The influence of femtosecond laser parameters on the degree of thermal denaturation was studied experimentally. The relationship between the degree of thermal denaturation and the characteristic parameters of skin microstructure and the secondary structure of skin tissue proteins in characterizing the degree of thermal damage was analyzed. The results showed the interaction of laser power, laser power, and scanning speed had a significant effect on the degree of thermal denaturation; greater degrees of thermal denaturation were associated with larger second‐order moments of the texture angle of the skin microtissue and smaller entropy values and contrast, indicating a greater degree of thermal damage; and higher peak temperature, the lower peak intensity of Raman spectra, decrease in the percentage area of α‐helix fitted curves and increase in the percentage area of β‐sheet and β‐turn fitted curves indicate that the protein is denatured to a large extent that means thermal damage is large.