Organic acid is an important flavor presenting substance in liquor, and its content directly affects the acidity of the spirits. In this paper, in order to further understand the content of organic acids and their metabolic pathways in the spirits samples of Qingxiang-type baijiu during the period of spirits production, based on the production process of Qingxiang-type baijiu and the requirements of the control, we used the principal component analysis to analyze the types and contents of organic acids contained in Qingxiang-type baijiu. The partial least squares regression model was used to establish a prediction model for the quantitative analysis of PLSR of organic acids in clear-flavored liquor. The quantitative method of GC-MS was combined with HS-SPME to detect the volatile flavor substances in the wine spirits and analyze the metabolism of the main organic acids during the fermentation process. The average concentration of various non-volatile organic acids in clear-flavored liquor was characterized by BSTFA derivatization combined with GC-MS analysis. Solving the PLSR quantitative analysis model for organic acids in clear-flavored white wine yielded that of the major organic acids in white wine, acetic acid, propionic acid, butyric acid, valeric acid, hexanoic acid, and isovaleric acid, were all above 0.9. The RMSEP of the model ranged from 0.086 to 0.425, and the RPD values ranged from 3.895 to 12.007. With good model fitting and high prediction accuracy, the model can be promoted and applied to the quantitative detection of trace organic fractions in baijiu or other important foodstuffs, and it has a wide applicability.