The invention relates to a method for extracting athomin with mustard seeds as the raw material. The method comprises the following steps: taking mustard seeds in brassica in cruciferae as the processing raw material, soaking the raw material in water after being crushed, and then rapidly and effectively obtaining crude product of athomin by a subcritical water extraction method. Because the subcritical water extraction technology is a novel environment-friendly extraction technology not using or rarely using organic solvent, when being in the subcritical state, water has certain dissolving capacity to semi-polar and non-polar organisms, the polarity, the surface tension and the viscosity of water can be changed by controlling the temperature and the pressure of subcritical water, so that the dissolving capacity of the subcritical water to the organisms can be greatly imoroved, therefore, the extraction efficiency is greatly improved, and the content of allyl isothiocyanate product in athomin is high. Compared with the prior art, the method has the advantages of simple technological line, reasonable technological condition, simple and safe reaction and operation, short reaction time, low solvent loss, low technological cost, and high implementation value and social and economic benefit.