Laser-induced plasma micromachining (LIPMM) can be used to fabricate high-quality microstructures of hard and brittle materials. The liquid medium of the LIPMM process plays a key role in inducing the plasma and cooling the materials, but the liquid medium is overheated which induces lots of bubbles to defocus the laser beam and reduce machining stability. In this paper, a comparative investigation on bubble behavior and its effect on the surface integrity of microchannels in three types of liquids and at different depths during LIPMM has been presented. Firstly, the formation mechanism of microbubbles was described. Secondly, a series of experiments were conducted to study the number and maximum diameter of the attached bubbles and the buoyancy movement of floating bubbles in the LIPMM of single-crystal silicon under deionized water, absolute ethyl alcohol, and 5.6 mol/L phosphoric acid solution with a liquid layer depth of 1–5 mm. It was revealed that the number and maximum diameter of attached bubbles in deionized water were the highest due to its high tension. Different from the continuous rising of bubbles at the tail of the microchannels in the other two liquids, microbubbles in 5.6 mol/L phosphoric acid solution with high viscosity rose intermittently, which formed a large area of bubble barrier to seriously affect the laser focus, resulting in a discontinuous microchannel with an unablated segment of 26.31 μm. When the depth of the liquid layer was 4 mm, absolute ethyl alcohol showed the advantages in narrow width (27.15 μm), large depth (16.5 μm), and uniform depth profile of the microchannel by LIPMM. This was because microbubbles in the anhydrous ethanol quickly and explosively spread towards the edge of the laser processing zone to reduce the bubble interference. This research contributes to a better understanding of the behavior and influence of bubbles in different liquid media and depths in LIPMM of single-crystal silicon.