To identify the green off-flavor compounds in Moutai-aroma type Baijiu, a method involving sensory-guided fractionation and metabolomics was developed for analyzing its characteristic off-flavor compounds. The samples were separated into volatile and non-volatile compounds by vacuum rotary evaporation. Liquid-liquid extraction and sensory analysis were performed on the volatile components with an intense green off-flavor, and the results showed that the green off-flavor compounds mainly existed in the neutral/alkaline components. A total of 94 flavor compounds were qualitatively and quantitatively identified in the volatile components by gas chromatography-mass spectrometry (GC-MS), the predominant ones being esters, alcohols and aromatic compounds. There were significant differences between normal and defective Baijiu as determined by Venn diagram and clustered heatmap analysis. Furthermore, a total of 15 major differential compounds with variable importance in the projection (VIP) > 1 were identified by orthogonal partial least-squares discriminant analysis. Among them, alcohol and ester compounds showed the most significant difference between the two Baijiu samples. Esters including ethyl lactate, ethyl 2-furoate and ethyl DL-2-hydroxycaproate, as well as higher alcohols including isoamyl alcohol, isobutanol and furfural were identified as the major green off-flavor compounds, and also important contributors to the bitterness and astringency of Baijiu. It is worth noting that ethyl 2-furoate and ethyl DL-2-hydroxycaproate were identified in Baijiu with green off-flavor for the first time; however, their flavor characteristics have yet to be further investigated. The results of this study provide a scientific basis for improving the quality of Moutai-aroma type Baijiu and also provide a reference for the analysis of characteristic flavor compounds in foods in the future.