The objective of this study was to evaluate effects of dark brown sugar on acrylamide and 5-hydroxymethylfurfural (HMF) levels in brown sugar cookies. Dark brown sugar was used as a raw material instead of sucrose, and chitosan, chitooligosaccharides, or calcium carbonate were added to investigate their effect on acrylamide and HMF mitigation. The results demonstrated that the higher the content of acrylamide in the dark brown sugar, the higher the amount of acrylamide produced in baked brown sugar cookies. The addition of dark brown sugar significantly increased the diameter and decreased the thickness of cookies, which induced more acrylamide formation. Therefore, the sucrose control cookies were harder and thicker than dark brown sugar cookies. The addition of 1% chitosan, chitooligosaccharide, or calcium carbonate did not reduce the acrylamide formation of the brown sugar cookies. The content of acrylamide and HMF in the sucrose control group was lower than that in dark brown sugar groups, and chitooligosaccharide increased the level of HMF. This is due to the fact that the content of reducing sugar in dark brown sugar is higher than that in sucrose, and dark brown sugar contains acrylamide. There was no difference in the concentration of reducing sugar between test and control cookies (p > 0.05). The L values of brown sugar were lower than those of sucrose cookies, especially for chitooligosaccharide addition (p < 0.05). The addition of chitooligosaccharide generated more Maillard reaction products and caramelization. The reducing power of dark brown sugar cookies was higher than that of sucrose control cookies. The baking industry should choose sucrose or dark brown sugar containing a low acrylamide content as an ingredient to prevent the final products from containing high levels of acrylamide.