A silicon-based vapor-liquid phase separating heat radiation chip and a preparation method thereof relate to a heat radiation chip of electronic components. The silicon-based vapor-liquid phase separating heat radiation chip and the preparation method thereof are provided to overcome the disadvantages of a silicon-based radiator and improve heat radiation efficiency of the silicon-based radiator.The heat radiation chip is in an upper and lower-layer structure, and is provided with an upper silicon slice and a lower silicon slice respectively, wherein the upper silicon slice is provided with a cooling liquid loading port, a liquid vaporizer and a gas microchannel; and the lower silicon slice is provided with a cooling liquid storage tank and a liquid microchannel. The preparation method has the following steps: 1), processing the front structure of the upper silicon slice; 2), processing the back structure of the upper silicon slice; 3), processing the lower silicon slice; and 4) aligning the upper silicon slice and the lower silicon slice for bonding.