This study investigates the effect of structural changes of collagen fibrils on the bonding durability of a total etch luting resin (Super-Bond C&B) and a self-etching luting resin (Panavia F 2.0) to dentin. An atomic force microscope (AFM) was used to observe structural changes of intact dentin collagen fibrils after acidic conditionings of two bonding systems. After 90 d water storage and 15,000 thermal cycles (TC) as artificial aging, micro-tensile bond strength (microTBS) was utilized to evaluate the bonding durability of the two bonding systems to dentin. microTBS after 1 d or 90 d water storage without TC were separately measured in control groups. A cross-banding periodicity of about 67 nm along collagen fibrils was seen on demineralized intertubular dentin surfaces in AFM images. For both luting resins, thermal cycling decreased (p < 0.05) microTBS of 1 d and 90 d, compared to controls. Scanning electron microscope and transmission electron microscopic examinations revealed that the top and bottom of hybrid layer (HL) were weak links in the bonding interface over time. The results suggest that the top of HL contains disorganized collagen fibrils from the smear layer which degrade over time. AFM results indicate that the demineralized intact collagen fibrils beneath the smear layer were not denatured during acidic conditioning. However, these collagen fibrils may be structurally unstable due to poor infiltration by resin or loss of resin protection within the HL over time, reducing the long-term microTBS. This process was accelerated by thermal fatigue cycling.