This study was focused on the optimal extracting conditions of dimethyl-$eta$-propiothetin as bioactive substance from green seaweed. Identification and quantification of dimethyl-$eta$-propiothetin were measured by headspace gas chromatography after conversion to dimethyl sulfide by treatment with saturated NaOH solution. Dimethyl-$eta$-propiothetin was extracted through various processes (solvent extraction, ultrasonication, boiling and autoclaving) from Ulva pertusa. The content of dimethyl-$eta$-propiothetin extracted by autoclaving treatment showed higher than that of various extraction methods. Dimethyl-$eta$-propiothetin content in extract of Ulva pertusa was 325,800 ng/g after autoclaving 121$^{circ}C$ for 45 min. Dimethyl-$eta$-propiothetin in exract of Ulva pertusa was comparative stable under low temperature. The retentions of dimethyl-$eta$-propiothetin content in extract of Ulva pertusa were 76.6~99.8% by incubation at 10~6$0^{circ}C$ for 2 hours. Chemical decomposition of dimethyl-$eta$-propiothetin was observed under laboratory conditions at pH values higher than 9.5.