Lithium-ion batteries have received a great deal of attention on the world stage due to their high-power density and superior electronic properties. Herein, a novel phase change composite separator was successfully fabricated into lithium-ion battery cells by microfluidic technology. The phase change material composite separator was manufactured with polyethylene (PE) as the base film and employing the crystalline phase change property of polyethylene oxide (PEO). The phase change solution was atomized and delivered to the surface of the separator using high-pressure inert gases, and then crystallized on the separator substrate by controlling the temperature difference. The capacity retention and capacity recovery of the manufactured phase change material composite separator cells were 96.9% and 97.8%, respectively. In addition, the cells demonstrated superior multiplier performance (~98% capacity retention at 1C). Additionally, the phase change material was introduced into the separator coating layer to increase the heat resistance of the separator, while the electrochemical performance was exceptional and the safety performance was favorable, thus alleviating the heat accumulation inside the battery at the source and effectively enhancing the safety of lithium-ion batteries.