An increase in non-enzymatic collagen matrix cross-links, such as advanced glycation end-products (AGEs), is known to be a major complication in human mineralized tissues, often causing abnormal fractures. However, degradation of mechanical properties in relation to AGEs has not been fully elucidated at the material level. Here, we report nanoscale time-dependent deformation and dimensional recovery of human tooth dentin that has undergone glycation induced by x-ray irradiation. The reduction in enzymatic collagen cross-linking and the increased level of AGEs with concomitant growth of disordered collagen matrix diminished creep deformation recovery in the lower mineralized target region. However, the elevated AGEs level alone did not cause a reduction in time-dependent deformation and its recovery in the higher mineralized target region. In addition to the elevated AGEs level, the degradation of the mechanical properties of mineralized tissues should be assessed with care in respect to multiple parameters in the collagen matrix at the molecular level.