A robust and sensitive isotope dilution UPLC-MS/MS method was established for the simultaneous analysis of acrylamide (AA), 5-hydroxymethylfurfural (HMF), and 2-amino-1-methyl-6-phenylimidazo[4,5-b]-pyridine (PhIP). A fairly good separation of three analytes was achieved within 4.5 min. High correlation coefficients (R2 > 0.9998) of the three compounds were obtained in their respective linear ranges. This method demonstrated low limits of detection (1.57 μg/L for AA, 0.61 μg/L for HMF, and 0.02 μg/L for PhIP) and limits of quantification (5.22 μg/L for AA, 2.03 μg/L for HMF, and 0.05 μg/L for PhIP). This method also demonstrated excellent quantification accuracy (99.02%-101.12%), precision (RSD < 6%), and recovery (82.83-119.92%) in the Maillard model systems and deep-fried meatballs. This work develops a fundamental method for the rapid simultaneous determination of AA, HMF, and PhIP in thermally processed foods that are both carbohydrates-rich and protein-rich, meanwhile providing technical support for the generation mechanism of various hazards.