Micropores fabricated on organic polymer films have a wide range of applications in fields such as microfiltration, new energy, and biomedical separation. The use of laser processing technology can complete the processing of micropores on the surface of ultrathin films with high precision, but there is still some difficulty in the processing of ultrathick films. In this paper, a picosecond ultraviolet (UV) laser was used to explore the high-precision manufacturing process of micropores on the surface of ultrathick polyimide (PI) films. The effects of laser power, laser frequency, and scanning speed on the cone angle and spatter deposition area of micropores’ fabrication on ultrathick PI were studied based on orthogonal experiments. The mechanism of processing micropores on ultrathick PI was analyzed by studying the deposition area and morphology of the spatter generated during the laser ablation process. It was found that high-quality micropores can be fabricated at low laser frequency and high power.