Thermal errors of machine tools account for 40–70% of machining errors, with motorized spindles and linear motors being the primary heat sources adversely impacting machine tools’ precision. This article aims to solve the issue of significant thermal errors brought about by numerous internal heat sources, complex heat transfer processes, and uneven temperature field distributions. This article proposes a cooling control strategy that employs multiple channels with varying water temperature and velocity. The article also presents the design of the cooling system for a machine tool. The established multi-channel cooling control equation is then used to optimize the cooling water parameters of different channels. Ultimately, finite element simulations and cooling experiments verify the system’s efficacy. Based on the data collected from simulations and cooling experiments, it has been demonstrated that the motorized spindle motor’s thermal balance temperature decreased by 58.5% after cooling, and the shaft deformation was reduced by 70.2%. Similarly, the linear motor’s thermal balance temperature decreased by 37.13%, and the parallelism error of the machine tool guide rail was reduced by 72.3%. These results demonstrate convincingly that the machine tool cooling system can achieve more accurate and efficient cooling, which can provide a reference for machine tool thermal error control technology.