A two-step combined processing technique, combining a continuous-wave laser with a waterjet-assisted nanosecond laser, has been introduced to enhance the quality and efficiency of laser micro-hole processing for nickel-based superalloys. Initially, a through-hole was created using a continuous-wave laser, followed by hole refinement with a coaxial waterjet-assisted nanosecond laser. In the first step, orthogonal testing methods were employed to investigate the impact of various parameters, including power, duty ratio, frequency, defocusing amount, and processing time, on the entrance and exit apertures, as well as the hole taper. Through the analysis of variance (ANOVA) method, the optimal parameter combination A2B1C4D3E1 was identified, achieving the minimal hole taper. This combination comprised a power level of 80 %, a duty ratio of 15 %, a frequency of 400 Hz, a defocusing amount of 2 mm, and a processing time of 10 ms. In the second step, a comparison was made between scanning and trepan drilling machining methods. The results unequivocally demonstrated that scanning drilling achieves superior entrance and exit morphologies. Furthermore, the effect of water jet velocity on the morphology of micropores was thoroughly analyzed. The voltage range of the water pump was adjusted from 10 V to 24 V, revealing that a voltage of 20 V produced the smallest hole taper. The scanning filling diameter was accurately preset according to the preformed hole aperture as well as the thickness of the recast layer. Finally, after coaxial waterjet-assisted laser precision machining, the inner wall of the hole is free of cracks, and the recast layer and oxide layer are effectively minimized. The initial hole prefabrication with the continuous-wave laser took merely 0.01 s, and the subsequent fine-tuning with the coaxial waterjet-assisted laser took 2 min and 25 s.