Storage is a key factor controlling the quality of Jiangxiangxing baijiu, and storage time and the type of storage container play crucial roles in shaping the baijiu's distinct flavor. To investigate the influence of storage containers on the flavor characteristics of Jiangxiangxing baijiu, the sensory qualities, flavor components, and metal ions of Jiangxiangxing baijiu were measured during 24 months of storage in a pottery jar or a stainless steel tank. The results showed that Jiangxiangxing baijiu preserved in a pottery jar was superior to that stored in a stainless steel tank. A total of 96 flavor substances were detected, and 17 key flavor characteristic substances were screened by combining the results of odor activity values (OAV) and orthogonal partial least squares-discriminant analysis (OPLS-DA). A correlation heat map and redundancy analysis (RDA) showed that aluminum, cadmium, iron, cobalt, magnesium, potassium, and copper ions promoted the formation of key characteristic substances including diethoxymethane, lactic acid, 2,3-dimethyl-5-ethylpyrazine, 1-hexanol, and 2-methyl-1-propanol. Overall, the results show that 24-month pottery jar storage can promote the flavor quality of Jiangxiangxing baijiu. This study established a theoretical foundation to select the appropriate storage conditions and control the flavor quality of Jiangxiangxing baijiu.