In the defense acquisition, a company’s goal is to maximize profits, and the government’s goal is to allocate budgets efficiently. Each year, the government estimates the ratio of indirect cost sector to defense companies, and estimates the ratio to be applied when calculating cost of the defense articles next year. The defense industry environment is changing rapidly, due to the increasing trend of defense acquisition budgets, the advancement of weapon systems, the effects of the 4th industrial revolution, and so on. As a result, the cost structure of defense companies is being diversifying. The purpose of this study is to find an alternative that can enhance the rationality of the current methodology for estimating the ratio of indirect cost sector of defense companies. To do this, we conducted data analysis using the R language on the cost data of defense companies over the past six years in the Defense Integrated Cost System. First, cluster analysis was conducted on the cost characteristics of defense companies. Then, we conducted a regression analysis of the relationship between direct and indirect costs for each cluster to see how much it reflects the cost structure of defense companies in direct labor cost-based indirect cost rate estimates. Lastly a new ratio prediction model based on regularized regression analysis was developed, applied to each cluster, and analyzed to compare performance with existing prediction models. According to the results of the study, it is necessary to estimate the indirect cost ratio based on the cost character group of defense companies, and the direct labor cost based indirect cost ratio estimation partially reflects the cost structure of defense companies. In addition, the current indirect cost ratio prediction method has a larger error than the new model.