Abstract: Program comprehensive design of geological engineering is one of important practical teaching processes in the course teaching system of geology in mining colleges. In order to cultivate geological talents to meet social development needs in the new era and improve undergraduate teaching quality, a program comprehensive design of geological engineering with distinctive "mining" features is being carried out for undergraduates. The main contents, implementation process and application of three-dimensional numerical modeling in the program comprehensive design of geological engineering were introduced in this article. Not only did the program comprehensive design of geological engineering improve students' practical ability of analyzing problems comprehensively and applying theoretical knowledge to solve practical problems, but also cultivated students' innovative thinking and spirit and laid a solid foundation for the cultivation of high-quality coal geological talents henceforth.