With the rapid development of the information age, electronic components are developing toward miniaturization, which makes the manufacturing of chips more and more difficult. Water jet-guided laser processing technology (WJGL) is a composite processing technology that combines pulsed laser and water jet, which can ensure the accuracy and efficiency of processing while small size parts machining. This paper is based on the “element birth and death” technique in the finite element method and the three-dimensional transient temperature field and subsequent material removal model of 6061 aluminum alloy are established. The effects of laser average power, pulse repetition frequency, and pulse action time on the transient thermal distribution, aperture, taper, and other forming qualities with the two technologies of fixed-point drilling and spiral drilling, respectively, are studied. Combining the experimental process, the general rule of morphology change of the micro-hole is obtained. The results show that WJGL of micro-hole is based on the combined effect of thermal ablation and real-time cooling. Spiral drilling can maintain a better hole shape but fixed-point drilling can achieve a smaller hole taper. With the increase of laser power, the hole taper increases, reaching saturation at 8 W. The repetition frequency is between 50 and 70 kHz to obtain better hole morphology while maintaining better processing efficiency, and the minimum hole taper is 8.21°.