Background: Recently, more chemical and biotechnological applications have been found in Kluyveromyces marxianus than Saccharomyces cerevisiae in the food field because they show advantageous metabolism features in the production of flavor components of interest. However, most of study demonstrated Kluyveromyces marxianus involved in ethanol synthesis in the dairy products in food fields. Our study aims to clarify the formation mechanism of ethyl acetate and organic acids in acid rice soup inoculated with Kluyveromyces marxianus.Results: The higher concentration of ethyl acetate than ethanol and organic acids in fermented acid rice soup inoculated with Kluyveromyces marxianus. Up-regulated genes/proteins, including ADH1, ADH2, ADH6, ATF1, ACCT, and TES1, and down-regulated ALD family involved in glycolysis/gluconeogenesis and pyruvate metabolism played the crucial roles in the formation of ethyl acetate and other esters. In addition, up-regulated genes/proteins involved in starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis, TCA cycle, and pyruvate metabolism played the important roles in the formation of organic acids, ethanol and esters.Conclusion: Our results reveals the formation mechanism of ethyl acetate and organic acids in acid rice soup inoculated with K. marxianus L1-1. This study provides the basis for improving aroma and taste of fermented foods and reveals the formation mechanisms of flavors in no-dairy products.