To investigate the formation pattern of dimethyl sulfide in shepherd’s purse, headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) was used to analyze the volatile flavor compounds of the whole and cut-up raw plants of shepherd’s purse as well as the cut-up boiled plants stored at different temperatures for different durations. The changes in the contents of dimethyl sulfide and its beneficial precursor, S-methyl-L-cysteine sulfoxide, were studied, and the formation mechanism of dimethyl sulfide was speculated. The results showed that alcohols such as (Z)-3-hexenol and aldehydes such as (Z)-3-hexenal were detected in fresh shepherd’s purse. The cutting process and storage temperature significantly affected the major flavor compounds in shepherd’s purse. A storage temperature of 25 ℃ and cutting was more prone to produce dimethyl disulfide in shepherd’s purse. In addition, liquid chromatography-mass spectrometry (LC-MS) analysis showed a significant decrease in S-methyl-L-cysteine sulfoxide. The Pearson correlation results showed a significantly negative correlation between the contents of dimethyl sulfide and S-methyl-L-cysteine sulfoxide in shepherd’s purse, suggesting that the dimethyl sulfide in shepherd’s purse might be formed through the enzymatic conversion of S-methyl-L-cysteine sulfoxide. This study clarified that cutting and storage temperature were key factors controlling the formation of dimethyl sulfide in shepherd’s purse, providing a theoretical basis for improving the flavor and nutritional quality of shepherd’s purse.