Safety hazards associated with separators in lithium-ion batteries are more pronounced in light of the significant improvement of energy density of batteries, hindering their wide application. In this research, asymmetric poly (vinylidene fluoride) (PVDF)-coated polyimide separators with three-dimensionally homogeneous microporous (3DHM API/PVDF) structure are prepared, in which a PVDF layer with a thickness of 6 μm on one side of polyimide. Polyimide, as the base film, has a high heat-resistant temperature which ensures that as-prepared separators will not be shrunk and burned. The coated PVDF layer imparts 3DHM API/PVDF with thermal shutdown function at 175 °C due to the melting of PVDF. The temperature difference between the shutdown and meltdown temperature is over 100 °C, ensuring that the LIB assembled with 3DHM API/PVDF is safe for use. Moreover, the interconnected microporous structure of the separator facilitates the formation of 3D Li+ transport pathways and uniformity of lithium deposition, suppressing lithium dendrite growth. The coin cells assembled by 3DHM API/PVDF exhibit similar electrochemical performance to that of a commercial polypropylene separator at room temperature. Therefore, the novel 3DHM API/PVDF separator may be a promising candidate for a significantly safer LIB.