We successfully designed a nanohybrid sensor based on carboxyl-functionalized multi-walled carbon nanotubes (MWCNTs-COOH) co-functionalized with both carboxymethyl cellulose (CMC) and chitosan nanosphere (CSN) for a simple, low-cost, highly-sensitive voltammetric recognition and determination of Methylglyoxal (MG) as chemical marker of New Zealand Manuka honey. Morphology and structure revealed that CSN-CMC was adhered onto MWCNTs-COOH surface. Interactions between modifying layers and both reduction potential and response mechanism of MG were confirmed by theoretical calculations. The nanohybrid sensor displayed large electrochemical effective area, excellent electrocatalytic activity, a wide linear range of 5 x 10(-8)-8 x 10(-4) mol/L, a low detection limit of 9.6 x 10(-9) mol/L, and good stability as well as selectivity under the optimal conditions. The applicability of the fabricated sensor was assessed using three Chinese honeys and one New Zealand Manuka honey. This work will put forward a new strategy for electrochemical recognition and detection of MG as chemical markers of many agricultural production, processing, products and food and a new alternative tool for assessing economically motivated fraud and counterfeit issues in Chinese honey markets using electrochemical nanohybrid sensor.