A newly developed microscopic Fourier transform infrared (FT-IR) spectrometry combined with differential scanning calorimetry (DSC) has been used to investigate simultaneously the thermal response and IR spectral changes in protein structure in porcine stratum corneum (SC) after pretreatment with skin penetration enhancers (propylene glycol (PG), azone/PG, oleic acid (OA)/PG, vitamin C, and vitamin C + OA/PG). The amide I and II bands of the protein were used as probes to determine its structural transformation with temperature. A reheating process was also performed. The dual effects of enhancer and temperature on the protein conformational changes of porcine SC were studied. The results indicate that the newly developed FT-IR/DSC system can continuously determine the thermoresponsive conversion process from alpha-helix to beta-sheet in the keratin structure of porcine SC pretreated with different enhancers. The temperature-induced keratin conversion in the protein structure of porcine SC was irreversible, with or without pretreatment with skin penetration enhancers. The conformational transition in the protein during heating was found to be partially from the alpha-helix to a random coil structure, and partially from the alpha-helix to the beta-sheet structure. The kinetics of this collversion for the first and second heating processes were significantly different; the conversion process for all the first-healed SC samples during the second heating process was slower than that of the samples during the first heating process. Moreover, it was found that the skin penetration enhancers were able to alter synergistically and promote keratin conversion in the protein structure of porcine SC when accompanying the heating process. PG, OA/PG anti azone/PG were found to be the most effective.