Ethyl carbamate is a potential carcinogenic compound derived from the spontaneous reaction of ethanol with urea and citrulline in Chinese rice wine. The strain Lactobacillus brevis 2-34 isolated from Chinese rice wine fermentation liquor showed high citrulline re-uptake capacity in both single and co-culture systems. The present study therefore supplemented this strain with starter inoculations in Chinese rice wine fermentation, with the aim to decrease citrulline and subsequent ethyl carbamate content. The final Chinese rice wine liquor contained less citrulline and ethyl carbamate, as well as several harmful higher alcohols, and more esters which contributed to flavors. Gene sequencing showed the presence of the dcuC and transporter genes, for which the encoded proteins may be responsible for citrulline transportation. This study showed a possible way to control citrulline and ethyl carbamate in Chinese rice wine and also showed some aspects of the citrulline transport mechanism.