This work aimed to investigate the effects of chlorogenic acid (CA) and vanillic acid (VA) on structural changes in myofibrillar protein (MP) and fluorescent advanced glycation end products (fAGEs) formation in low-temperature-processed pork meat. Raw pork was prepared, different concentrations (0, 0.005%, 0.010%, 0.020%, 0.040%) of CA or VA were added, and then heated at 50 °C for 12 h. The results suggested that the degree of lipid oxidation significantly declined with increase in amounts of CA (from 12.166 ± 0.469 to 4.661 ± 0.333) or VA (from 11.771 ± 0.355 to 5.451 ± 0.362), and carbonyls, surface hydrophobicity, tryptophan fluorescence intensity, and protein oxidation products also showed a significant downward trend (p < 0.05). Compared with the control (498.183 ± 10.849), there were marked decrease of fAGEs intensity in samples containing CA (70.958 ± 4.114) or VA (76.667 ± 3.882). Besides, mitigating capacity of CA on fAGEs accumulation was just greater than that of VA. Therefore, CA and VA can impede MP and lipid oxidation of raw pork, which further reduce fAGEs formation in low-temperature-processed pork meat. This study is expected to provide a new strategy to prevent the oxidation of MP and reduce fAGEs contents in the meat industry.