<p>Throughout the aging progression, the alterations in chemical constituents hold a vital position in determining the quality of yellow rice wine. In the present research, the conventionally brewed yellow rice wine from Shaoxing area was selected as the subject of investigation. High performance liquid chromatography (HPLC) was employed to assay the amounts of organic acids and free amino acids within yellow rice wine samples corresponding to diverse aging durations. By integrating principal components analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) methodologies, the effect of aging time on the concentrations of organic acids and amino acids in yellow rice wine was explicated. The findings indicated that as the aging time lengthened, the overall quantity of organic acids in yellow rice wine manifested a descending tendency. The overall amount of free amino acids initially declined and subsequently rose. Three characteristic substances (tartaric acid, pyruvic acid, and glycine) with pronounced disparities (<i>P</i> &lt; 0.05, VIP ≥ 1) were identified. In summary, this proposed exploration has augmented the comprehension of the dynamic transformation mechanism of organic acids and free amino acids during the aging process of yellow rice wine and shed new insights for enhancing the quality management of yellow rice wine.</p>