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As a natural carrier protein, zein was intensively studied for the construction of a flavonoid delivery system. Chrysin has presented superior tumor‐resistant, anti‐inflammatory, and anti‐oxidation potentials among the flavonoid candidates in clinical practice. However, due to inadequate research, the binding mechanism and structural affinity of zein to chrysin are still indeterminate. Therefore, multispectral methods were employed to explore the molecular interaction of zein and chrysin in this work. These techniques showed that chrysin reduced the intrinsic fluorescence of zein via a static process and that the interaction between zein and chrysin was mainly driven spontaneously by hydrophobic forces. Additionally, the experimental results revealed the changed microenvironment in the vicinity of tyrosine and affected secondary structure in the presence of chrysin, indicating zein's conformation were altered by chrysin. This work provided comprehensive insight into the combination of plant‐derived protein (zein) and flavonoids (chrysin) and helped rationalize the protection, transportation, and release of chrysin through a zein‐based delivery system. [ABSTRACT FROM AUTHOR]