A Q-switched Nd:YAG laser is used to fabricate micro channels in a fused silica substrate by thermal induced processing and laser-induced plasma processing. The length of micro channels by thermal induced processing can be controlled and there are many thermal cracks around the channel. The interior wall of the micro channels drilled by laser-induced plasma is smooth, and the depth of the channel is up to 4 mm. The temperature and thermal stress distributions of thermal induced processing are calculated, and the behavior of laser-induced plasma processing is studied. The results indicate that as a result of great temperature changes, the thermal stress is larger than the fracture strength of sample, which leads to the formation of the channel and the thermal cracks. The ablation of the high temperature plasma formed by plasma shielding effects leads to a micro channel of high quality with a smooth internal surface and no thermal cracks.