Abstract: In order to investigate the stability of allyl isothiocyanate in water, four important factors, temperature, time, pH and ultrasonic frequency, were selected to design orthogonal experiments. The isothiocyanate was dissolved in an aqueous solution containing a small amount of methanol. The effects of the different factors on its stability were characterized by the changes of allyl isothiocyanate concentration determined by HPLC. The results showed that the affects of the time on allyl isothiocyanate degradation were most significant, followed by ultrasonic frequency, temperature and pH. After petroleum ether was used to extract the degradation mixture, The LC-MS and GC-MS analysis data suggested that allyl thiocyanate and cyclopropyl isothiocyanate were main products of allyl isothiocyanate degradation, and with the degradation of allyl isothiocyanate, their quantity increased.