The purpose of this study was to characterize essential changes in the structure of annulus fibrosus (AF) after hydrothermal and infrared (IR) laser treatment and to correlate these results with alterations in tissue state. Polarization-sensitive optical coherence tomography imaging was used to measure collagen birefringence in AF. Differential scanning calorimetry was used as a complementary technique, providing detailed information on thermodynamic processes in the tissue. Birefringence, peak of the denaturation endotherm, and the enthalpy of denaturation (ΔHm) were determined before and after hydrothermal heat treatment (85°C for 15 min) and non-ablative Er:glass fiber laser exposures on AF in the whole disk (vertebrae-disk–vertebrae complex). Our data have demonstrated quantitative differences between results of laser and hydrothermal heating. Birefringence did not disappear and ΔHm did not change after treatment in the water bath, but loss of birefringence and a decrease in the enthalpy did occur after laser exposure. These results could be explained by the photomechanical effect of laser irradiation. We suggest that thermo-mechanical stress played a dominant role in the disruption of the collagen network of AF under non-homogeneous laser heating.