The invention belongs to the technical field of semiconductor manufacturing, in particular to a high-precision silicon-based through-hole mask split pattern structure. The through-hole mask plate split pattern structure of the invention takes a double-sided polished silicon wafer as a substrate and comprises a front pattern and a back pattern. The front pattern includes a high-precision pattern with alignment marks and a low-precision pattern with alignment marks separated from the overall pattern, or a plurality of groups of different precision patterns with alignment marks respectively. Thereverse figure, which is a square covering all the figures on the front, is used to reduce the overall thickness; In the machining process of through-hole mask, high-precision pattern and low-precision pattern are used successively, and the same alignment marks are used to align the positions of the two patterns, so as to complete the machining of the whole pattern. The high-precision silicon-based mask plate designed by the invention has the advantages of high mechanical strength, high reusability, low cost, free and flexible graphic design and the like, and can meet the requirements of various fields for the high-precision through-hole mask plate.