[Background] White pellicle was always visible on the surface of soybean paste, which seriously decreasing consumers’ desirability and thus leading to an enormous waste of the product. [Objective] This study was designed to avoid the emergence of white pellicle in soybean paste by developing novel, safe and targeted control strategies. [Methods] First, the microstructure of white pellicle was visualized by light microscope. Second, microorganisms were selected from white pellicle using the YPD medium containing 18% NaCl. Then, species of these selected microorganisms were identified according to ITS (Internal transcribed spacer) sequence analyses and carbon source utilization experiments. Finally, the molecular mechanisms of white-pellicle-formation were analyzed. [Results] The white pellicle was visualized as repeated, round and movable body by light microscope and microorganisms which were selected from the white pellicle were identified as velum-forming Zygosaccharomyces rouxii. On the one hand, when oxygen was restricted, the transcription of ACS2 (a lipid biosynthetic gene) and FLO11 could be inhibited, and the reduction of lipid synthesis rate may have a negative effect on the propagation of yeast, and thus the production of the white pellicle was inhibited. On the other hand, the addition of 2% bioethanol can significantly enhance the transcription of protein transport-coding gene BTN2, and thus prevented the formation of white pellicle, eventually. [Conclusion] The study revealed the cause of white pellicle in soybean paste and proposed targeted strategies for the control of white pellicle without reducing the flavor and taste, which provided a new idea for the storage and consumption of soybean paste and other high nitrogen fermented products.