During the conventional production of brown fermented milk (BFM), unhealthy substances (3-deoxyglucosone (3-DG), methylglyoxal (MGO), and 5-hydroxymethylfurfural (HMF)) are generated during the Maillard browning step. Here, an alternative browning process based on the hydrolysis of endogenous lactose was established. Compared with the conventional process, 3-DG and HMF were decreased by 5.91 mg kg-1 and 0.39 mg kg-1 in the brown milk base under the alternative browning process, and thereafter, 3-DG and HMF were decreased by 54.5% and 65.0% in BFM. Investigation into the formation of 3-DG, MGO, and HMF in different chemical models showed that different sugars lead to different Maillard reaction products and browning rates, contributing to the mitigation of 3-DG and HMF. Apart from the mitigation of unhealthy Maillard compounds, hydrolyzing lactose and avoiding the addition of external glucose make the alternative browning process a theoretical and practical basis for improving the quality and safety of BFM.