Baking processing is indispensable to determine special sensory prosperities of cookies and induces the formation of some beneficial components such as antioxidants. However, the formation of some Maillard reaction-derived chemical hazards, such as acrylamide (AA) and N(ε) -(carboxymethyl) lysine (CML) in cookies is also a significant consequence of baking processing from a food safety standpoint. This study investigated the effects of baking conditions on the formation of AA and CML, as well as the antioxidant activity (AOA) of cookies. Cookies were baked at various baking temperatures (155 to 230 °C) and times (1.5 to 31 min). AA and CML contents were determined by ultra-performance liquid chromatography-tandem mass spectrometry, respectively. The highest level of AA was obtained in the cookies baked at 155 °C/21 min and 205 °C/11 min (328.93 ± 3.10 μg/kg and 329.29 ± 5.29 μg/kg), while the highest level of CML was obtained in the cookies baked at 230 °C/1.5 min (118.05 ± 0.21 mg/kg). AA was prone to form at relatively low temperature range (155 to 205 °C), however, CML at relatively high temperature range (205 to 230 °C). The CML content was much higher than the AA content in the same set of cookies, by about 2 to 3 orders of magnitude. The AOA of cookies increased at more severe baking conditions. According to the AA and CML content, AOA and sensory properties of cookies, the temperature-time regime of 180 °C/16 min might be a compromised selection. However, only optimizing the baking condition was not enough for manufacture of high-quality cookies. Cookies, a kind of widely consumed bakery products in the world, contain some potentially harmful compounds, like acrylamide (AA) and N(ε) -(carboxymethyl) lysine (CML). AA in cookies has led to public health concern and several research efforts. But CML, another Maillard reaction-derived chemical hazard, has been neglected so far, even though its content is much higher than that of AA in cookies. The results contribute to further insight into the Maillard reaction and are useful for the selection of baking conditions to produce high-quality cookies with lower AA and CML contents, higher AOA, and better sensory properties.