In the present study, citrus peels were extracted using various conventional and deep eutectic solvents (DESs). Compared to other citrus peel extracts, the DES extract based on choline chloride showed notably higher total phenolic and flavonoid content levels, along with superior antioxidant activity, among these extracts. Consequently, this study aimed to further investigate the inhibitory effects of the choline chloride based DES extract on the production of both free and bound heterocyclic amines (HAs) and advanced glycation end products (AGEs) in roast pork meat patties. The results indicated that the addition of choline chloride-based DES extracts, particularly the choline chloride-carbamide based DES extract, can effectively reduce the oxidation of lipids and proteins by quenching free radicals. This approach proves to be the most efficient in reducing the formation of both HAs and AGEs, leading to a significant reduction of 19.1–68.3% and 11.5–66.5% in free and protein-bound HAs, respectively. Moreover, the levels of free and protein-bound AGEs were reduced by 50.8–50.8% and 30.5–39.8%, respectively, compared to the control group. Furthermore, the major phenolics of citrus peel extract identified by UHPLC-MS were polymethoxylated flavonoids (PMFs) including hesperidin, isosinensetin, sinensetin, tetramethoxyflavone, tangeretin, and hexamethoxyflavone, which inferring that these compounds may be the main active ingredients responsible for the antioxidant activity and inhibition effects on the formation of HAs and AGEs. Further research is needed to explore the inhibitory effects and mechanisms of PMFs with different chemical structures on the formation of HAs and AGEs.