Substandard and counterfeit anti-diabetic medicines directly influence the health and impose a great danger to individual patients and to public health. Counterfeiting has become a serious and underreported problem in the pharmaceutical industry. There are a large number of counterfeit medicines flooded in anti-diabetic markets which effect human health directly and indirectly. Therefore, some novel analytical techniques are necessary to be established for detecting these counterfeit drugs. In this study, a novel skeleton type molecularly imprinted column was successfully prepared. Based on the column, a simple, fast and reliable two-dimensional chromatography analytical system was established for selective determination of the illegal sulfonylurea additive in traditional Chinese patent medicines and functional foods. The developed method was validated. The linearitiesof the method were tested with calibration curves using ten calibration points in the concentration range of 0.25–12.5 μg/g. The LODs were 0.0125 μg/g and 0.01 μg/g for tolbutamide and glibenclamide respectively. The five batches of Chinese patent medicines and dietary supplements obtained from different markets and online websites were tested by the validated method. With good retention time and spectral confirmation, chemical anti-diabetic substances were identified and quantified in traditional Chinese medicine and in dietary supplements.