Response surface methodology (RSM) is a statistical approach widely used in food processing to optimize the formulation, processing conditions, and quality of food products. The homogenization process is achieved by subjecting milk to high pressure, which breaks down fat globules and disperses fat more evenly throughout milk. This study focuses on an application of RSM including the logit transformation to predict the efficiency of milk homogenization, which can be maximized by minimizing the relative difference in fat percentage between the top part and the remainder of milk. To avoid a negative predicted value of the minimum of this proportion, the logit transformation is used to turn the proportion into the logit, whose possible values are real numbers. Then, the logit values are modeled and optimized. Subsequently, the logistic transformation is used to turn the predicted logit into the predicted proportion. From our model, the optimum condition for the maximized efficiency of milk homogenization was predicted as the combination of a homogenizer pressure of 30 MPa, a storage temperature of 10℃, and a storage period of 10 days. Additionally, with a combination of a homogenizer pressure of 30 MPa, a storage temperature of 10℃, and a storage period of 50 days, the level of milk homogenization was predicted to be acceptable, even with the problem of extrapolation taken into account.