The invention discloses a drilling tool selection method. The method comprises the following steps: obtaining a number of needed drilling tools and a number of stocked drilling tools, and comparing the number of needed drilling tools with the number of stocked drilling tools; if the comparison result indicates that the number of stocked drilling tools is greater than or equal to the number of needed drilling tools, extracting drilling tools from a drilling tool magazine; if the comparison result indicates that the number of stocked drilling tools is smaller than the number of needed drilling tools, buying drilling tools to supplement the drilling tool magazine. According to the drilling tool selection method, the drilling tool selection correctness and efficiency can be improved, the drilling tool selection automation can be realized, the production efficiency can be improved, the artificial participation in the production process can be decreased and the workload of the workers can be decreased. Moreover, the invention provides a PCB hole drilling system which adopts the drilling tool selection method and is high in hole drilling efficiency and correctness.