Biscuits are a type of baked food popular among consumers. However, recent studies have found that the associated hazards of monochloropropanediol esters (MCPDEs) and glycidyl esters (GEs) are widely present in biscuits, potentially threatening human health. In this study, L-cysteine, a bread quality improver used in food, was selected as an additive to inhibit the formation of MCPDEs and GEs in biscuits. Its addition effectively reduced the contents of 3-MCPDEs, 2-MCPDEs, and GEs in biscuits, and its inhibition efficiency increased with the its amount. The inhibition efficiencies of 3-MCPDEs, 2-MCPDEs, and GEs in biscuits when the mass fraction was 0.08% were 35.89, 33.97, and 30.98%, showing higher inhibition efficiency than that of TBHQ. The addition of L-cysteine enhanced the antioxidant activity, improved surface brightness, and increased crispiness of the biscuit. Furthermore, its addition affected the flavors of biscuits, wherein the contents of volatile aldehydes, ketones, acids, alkanes, and olefins decreased, but the contents of esters, aromatic hydrocarbons, and pyrazines increased. This study provides new ideas for the development of new low-hazardous substance biscuits.