Many firms have applied flexible manufacturing systems as a means of increasing productivity, profitability, and quality. Therefore, the purpose of this paper is to develop the more efficient justification model through an analytical scoring model with the quantitative factors, flexibility factors, and safety factors under uncertainty. In this paper, the three factors for properly comparing and evaluating of flexible manufacturing systems are presented. Especially, this paper has emphasized the flexibility and safety factor; the one consists of organization assessment, process treatment function, products and products quantity, useful life assesment, and software function, the other presents risk assesment, Y2K problem, safety device analysis, total productive management system, safety management. Finally, a normalized scoring model by the new flexibility and safety factors can be used in real fields for flexible manufacturing systems project selection under uncertainty.