Risk communication is the key to ensure risk decision-making in a scientific and proper way. Based on the analysis on risk communication in the process of awarding security certificate of transgenic rice in China, this paper concludes that risk communication in controversial S&T decision-making is not enough and the main reasons include poor awareness in risk communication, narrow scope of participants and insufficiency of response mechanism. Therefore, this paper proposes several suggestions on how to perfect risk communication mechansim in China’s S&T decision-making, such as strengthening awarness of risk communication, positively responding to problems of public interest, institutionalizing public participation and carrying out accountability system for faulty decision-making.