In this paper, we focussed on the processing power of CO2 laser systems and the impact of scanning speed, scanning power and number of scans on the quality of microchannels. We created microchannels which are based on the Koch fractal principle through a flexible and low-cost CO2 laser system. The processing and manufacturing method of Koch fractal micromixer on polymethyl methacrylate (PMMA) substrate was also studied. The microchannel structure based on the Koch fractal principle can increase the contact area and mixing time of the fluid and improve the mixing efficiency of the micromixer. In the experiment, our speed is 2, 4 and 6mm/s, the number of scans is 2/3/4 times and the power is 4, 8 and 12W. As the power and number of scans increase and the speed decreases, the width and depth of the microchannel are changed more clearly, which contributes to the successful thermal bonding of the Koch fractal micromixer and avoids thermal bonding due to overvoltage. By comparing the experimental data, we found that the width and depth of the channel are ideal when the speed is 2mm/s, the number of scans is 4 and the power is 12W. Because of the lower cost of PMMA, the use of CO2 laser systems to fabricate microchannels on PMMA substrates will have broad application value, reduce cost and be easier to manufacture.