Methylglyoxal (MGO) is the primary material basis for the non-peroxide antibacterial activity (NPA) of manuka honey from New Zealand. Therefore, it is necessary to identify the quality or discriminate the grade of honey because no all manuka honeys on the market display the NPA. The current routine method employed for the detection of MGO involves high-performance liquid chromatography (HPLC) test. However, it requires long time (∼8 h) for sample derivatization. Herein, we report an intrinsic Raman signal amplification strategy for the rapid identification and detection of MGO by using silver-coated gold nanoparticles (Au@Ag NPs) along with a high selective surface-enhanced Raman scattering (SERS) probe 8-thioguanosine (8-TG). 8-TG is synthesized via the derivatization of 8-bromoguanosine (8-BG) with thiourea, and its Raman peak assignments were confirmed by computer simulation. The detection is performed through the Raman intensity ratio (I631/I700) variation of N2-(1-carboxyethyl)-thioguanosine (CETG) formed by the reaction between 8-TG and MGO on surface of Au@Ag NPs, where one CETG Raman intensity at 631 cm−1 increases while the other one at 700 cm−1 decreases oppositely. The opposite change not only yields an intrinsic Raman signal amplification, but also provides built-in correction. As a result, the proposed SERS method exhibits high sensitivity and accuracy. In addition, the whole analytical test is achieved within ∼20 min. The method can be used for the fast detection of MGO in manuka honey and discrimination of the honey grade.