Baijiu quality control has always been a major challenge for researchers. In this paper, taking furfural which is closely related to baijiu brewing process and organic acids related to baijiu fermentation process and microorganism types as the main discriminating factors, a carbon dot (CDs) sensor array targeting furfural and organic acids was constructed to identify 41 kinds of baijiu. Through the fluorescence response investigation of CDs synthesized by isomers of benzenediol, aminophenol, and phenylenediamine to different baijiu, two CDs synthesized by meta‐benzene substitutions containing ‐NH2 were selected to build a fluorescence sensor array. Due to the aggregation‐induced enhancement effect between furfural and the CDs, and the protonation of organic acid and the CDs, different fluorescence changes were observed, the sensor array combined with partial least squares regression could quantitatively analyze furfural and organic acids. What is more, semi‐quantitative analysis of furfural and lactic acid in baijiu was performed. Owing to the interaction of the two CDs with furfural and organic acids in baijiu, the sensor array could accurately identify different baijiu through linear discriminant analysis. This sensor array has potential applications in the quantitative analysis of flavor substances in other alcoholic beverages, moreover, this method could provide a quick response and practical tool for real‐time quality control monitoring in the baijiu industry.