Nickel-based superalloys, serving as the preferred materials for hot-end structural components in aerospace engines, pose considerable challenges for the fabrication of high-quality gas film holes on their surfaces due to their inherent high hardness and strength. Water-jet-guided laser processing technology has exhibited notable potential in the realm of gas film hole fabrication; however, its engineering application is hindered by the lack of synergy between processing quality and efficiency. To tackle this issue, this study achieves efficient coupling between a 1064 nm high-power laser and a stable water jet, leveraging a multi-focal water–light coupling mode. Furthermore, an “inside-to-outside” multi-pass ring-cutting drilling strategy is introduced, and the controlled variable method is employed to investigate the influence of laser single-pulse energy, scanning speed, and pulse frequency on the surface morphology and geometric accuracy of micro-holes. Building upon this foundation, micro-holes fabricated using optimized process parameters are analyzed and validated using scanning electron microscopy and energy-dispersive spectroscopy. The findings reveal that single-pulse energy is a pivotal parameter for achieving micro-hole penetration. By moderately increasing the scanning speed and pulse frequency, melt deposition and thermal accumulation effects can be effectively mitigated, thereby enhancing the surface morphology and machining precision of micro-holes. Specifically, when the single-pulse energy is set at 0.8 mJ, the scanning speed at 25 mm/s, and the pulse frequency at 300 kHz, high-quality micro-holes with an entrance diameter of 820 μm and a taper angle of 0.32° can be fabricated in approximately 60 s. The micro-morphology and element distribution of the micro-holes affirm that water-jet-guided laser processing exhibits exceptional performance in minimizing recast layers, narrowing the heat-affected zone, and preserving the smoothness of the hole wall.