To realize the laser marking of Si wafers with clear identification and high cleanliness, this paper focuses on developing a laser marking process that is clear, splash free, debris free, and deep enough to meet the requirements of the subsequent processing process of semiconductor wafers. A 532 nm laser is used to study the influence of laser process parameters such as average power, pulse repetition frequency, and scan speed on laser marking of the Si wafer. The clarity, the depth, the height of the bump, and the heat affected zone of laser markings are evaluated by visual inspection, microscope, and white light interference three-dimensional profilometer. The research shows that compared with the low pulse frequency level below 50 kHz, the influence of average power and scan speed on the laser marking are lower. In the process window with average power 20%, pulse repetition frequency 60~80 kHz, and scan speed of 2 500~3 500 mm·s-1, parameter combination can be optimized to realize clear identification, no splash, and debris pollution laser marking on the silicon wafer, and the laser marking dots depth is 0.5~5 μm and the bump is less than 1 μm.