Texture on a mono-crystalline silicon substrate can effectively enhance the light trapping, and increase the short-circuit current of silicon hetero-junction solar cell. However, when the amorphous silicon layer deposited on the crystalline silicon substrate, the amorphous and crystalline epitaxial growth of mixed phases is created in the valleys with sharp edges, which leads to reducing the output characteristic parameters of the solar cell. In this paper, we use two methods to modify the microstructure of the textured substrate, and apply them to the silicon heterojunction solar cell. The textured silicon substrate is smoothed through the mixed acid, which makes the pyramid shape become round off and the open circuit voltage of the solar cell change from 564.6 mV to 609.4 mV. In addition, we use tetramethyl ammonium hydroxide (TMAH) instead of alkali solution. It is found that the textured substrate has an effective light trapping, and its micro-morphology is more rounded, the short-circuit current and open circuit voltage of the solar cell have been improved significantly.