This study conducted the logistics regression analysis in order to understand the recognition of Korean companies on the logistics security assurance programs such as AEO and ISO 28000 with respect to supply chain security. For this, the eight explanatory variables for the logistics regression model were identified by the exploratory factor analysis, and they were categorized into two groups such as positive and negative sides. The positive side consists of five factors such as visibility improvement, the sales capacity enforcement, efficient operating management, the reduction of customer complaint, and simplified customs clearance. The negative side has three factors such as the burden of expenses, the lack of partner collaboration, and institution irrationality. Then, the binominal outcomes(adopt vs. do not adopt) as dependent variables were set for indicating the intention on the choice of logistics security assurance programs. The results of logistics regression model showed that the companies recognized the AEO as a program to give simplified customs clearance and the sales capacity enforcement; instead, ISO 28000 could give them visibility improvement, the reduction of customer complaint, and efficient operating management. In addition, we found that all the companies had awareness on the institution irrationality in the inefficiency of operating security assurance programs regardless of the preference of AEO or ISO 28000. This implies that most companies want to enhance their competitiveness through not only the advantage of simplified customs clearance by AEO but also the efficient management system by ISO 28000. Therefore, the government needs to take into account the complementary operating strategy of both security assurance programs for improving the efficiency of the national logistics security system.