The aim of the present study was to evaluate the effect of chitosan and carboxymethyl chitosan (CMCS) on dentin surface morphology and bonding strength after irradiation of Er:YAG laser. Eighty-four laser-irradiated dentin samples were randomly distributed into three groups (n = 28/group) according to different surface conditioning process: deionized water for 60s; 1wt% chitosan for 60s; or 1wt% CMCS for 60s. Two specimens from each group were subjected to TEM analysis to confirm the presence of extrafibrillar demineralization on dentin fibrils. Two specimens from each group were subjected to morphological analysis by SEM. Seventy-two specimens (n = 24/group) were prepared, with a composite resin cone adhered to the dentin surface, and were then randomly assigned to one of two aging processes: storage in deionized water for 24h or a thermocycling stimulation. The shear bond strength of laser-irradiated dentin to the resin composite was determined by a universal testing machine. Data acquired in the shear bond strength test was analyzed by one-way ANOVA with the Tukey honestly significant difference post hoc test and Independent Samples t-test (α = 0.05). CMCS group presented demineralized zone and a relatively smooth dentin surface morphology. CMCS group had significantly higher SBS value (6.08 ± 2.12) without aging (p < 0.05). After thermal cycling, both chitosan (5.26 ± 2.30) and CMCS group (5.82 ± 1.90) presented higher bonding strength compared to control group (3.19 ± 1.32) (p < 0.05). Chitosan and CMCS group preserved the bonding strength after aging process (p > 0.05). CMCS has the potential to be applied in conjunction with Er:YAG laser in cavity preparation and resin restoration.