The paper investigates the characteristics of the laser beam percussion micro-drilling (LBPMD) process in aerospace nickel-based superalloy Hastelloy X using microsecond pulses. The quality of the drilled hole is crucial in laser beam micromachining, and selecting appropriate process parameters significantly impacts the hole’s quality. The objective is to achieve predefined hole dimensions with minimal taper angles. Additionally, the study focuses on the alteration of pulse width, which is a combination of laser pulse frequency and duty cycle. Laser power (P), duty cycle % (D), focal plane position (FPP), and laser frequency (f) are considered input parameters, while geometric features such as inlet and outlet diameters, hole taper angle, and inlet circularity are examined as process responses. ANOVA is employed to establish significant relationships between process parameters and response variations based on experimental tests. Creating a precise simulation model that accurately accounts for the moving boundary of the target material’s receding surface is a crucial and challenging task in formulating the laser heat conduction problem. It is necessary to simultaneously capture the material’s dynamic front movement and update the boundary conditions of the laser source. To model the micro-drilled hole with LBPMD, the UMESHMOTION and DFLUX subroutines, along with the arbitrary Lagrangian-Eulerian (ALE) adaptive remesh algorithm in the Abaqus™ software, are utilized. Notably, no previous numerical study has predicted the geometry of micro-drilled holes using this technique. The proposed procedure is validated through the predictions of inlet and outlet hole diameters. Special emphasis is placed on the validation of models. Consequently, the numerical model and statistical model are compared as well as the need to define model applicability. The study demonstrates that all input parameters significantly influence the inlet hole diameter, while the pulse width notably affects the taper angle and circularity. The interaction between high laser frequency and low duty cycle results in reduced pulse duration. Multi-objective optimization is performed to determine the optimal process parameter settings for desired quality characteristics, considering minimum hole taper angle, precise inlet diameter, and maximum inlet circularity of the hole as optimization criteria. The findings show that with the optimized predicted results obtained from the optimal input variables, a composite desirability of 92% can be achieved.