Abstract: Based on the meso-structure of concrete, the algorithm of three-dimensional numerical model for micro-scale concrete was studied by VC++ program code. A three-dimensional random aggregate generated and threw program was compiled by a new kind of algorithm according to analysis of related algorithms based on the former investigation. The planning of the numerical experiment was founded based on the orthogonal array, which allowed simulation to run with three parameters at three levels each. The three parameters chosen for this study were: velocity, the strength of aggregate and the modulus of aggregate. The results of numerical simulation show that the three parameters have different impact form and level on penetration performance.