A process integrating the extraction and transesterification of lipid from jatropha kernel powder for the production of biodiesel with methanol assisted by hexane is reported in this paper. The effects of catalyst amount, reaction time, reaction temperature, and siphon tube height on the yield and characteristics of biodiesel were investigated. It was found that hexane played the role of both co-solvent and co-extractant, which enhanced the efficiency of lipid extraction and the formation of a single phase containing methanol and lipid, facilitating mass transfer. Therefore, the reaction system had liquid-flow-solid-catalyzed character. The flow velocity of extraction liquor was controlled to fit for the rate of transesterification via controlling the reaction conditions. The products containing 80.2% fatty acid methyl ester (FAME) were obtained and its high heating value was 37.43MJ/kg. In this process, the residue of kernel powder, catalyst and products were simultaneously separated.