The present invention provides a numerical analysis model data generating program, method, and system for generating numerical analysis model data, which is used for numerical analysis, on the basis of three-dimensional shape data of a structure that is an object of analysis. Three-dimensional shape data defining the structure is inputted. Holes included in the inputted three-dimensional shape data are extracted, and the size of each of the holes is calculated. If the size of a given hole is smaller than a predetermined size, the hole is filled. Thus, numerical analysis model data is generated. According to the present invention, when the numerical analysis model data is generated, a relatively small amount of analysis model data can be generated without adversely affecting the accuracy in numerical analysis.