A computer-aided construction of molecular structure model for coal organic materials is proposed in this paper. In this method, the chemical fragments of coal organic materials are obtained by using the structural data of typical Japanese bituminous Akabira coal. First, some partial structures are selected from candidates of the structure, which are constructed by connecting input fragments based on construction knowledge from basic chemical experiments and practical experiments. Next, the partial structures are narrowed down to an appropriate one in terms of three-dimensional conformation by using partial structure evaluation. We found that this method can derive molecular structures more scientifically and in more time-saving way than the handmade structures.