Cooling system has an important role in the injection molding process in terms of not only productivity and quality, but also mold-making cost. In this paper, a conformal cooling channel with an array of baffles is proposed for obtaining uniform cooling over the entire free-form surface of molded parts. A new algorithm for calculating temperature distribution through molding thickness, mold surface temperature and cooling time was presented. The relation among cooling channels' configuration, process parameters, mold material, molding thickness and temperature distribution in the mold for a given polymer is expressed by a system of approximate equations. This relation was established by the design of experiment and response surface methodology based on an adequate physical-mathematical model, finite difference method and numerical simulation. By applying this approximate mathematical relation, the optimization process for obtaining target mold temperature, uniform temperature distribution and minimizing the cooling time becomes more effective. Two case studies were carried out to test and validate the proposed method. The results show that present approach improves the cooling performance and facilitates the mold design process in comparison to the trial-and-error simulation-based method.