This study aims to derive practical suggestions to apply application methods by auxiliary costs, especially application of logistics and customs clearance areas in order to establish EPS support system of auxiliary cost occurred from export/import. For the propose, this study has analyzed types and situation of auxiliary costs, application method by auxiliary costs, payment situation of logistics auxiliary costs and clearance auxiliary costs and suggested the relevant problems and their application methods. Especially, in case of logistics auxiliary costs through connection to the attached general documents required for negotiation by reflecting characteristics of B2B transactions. In addition, it has suggested that those services by the said system should be conveniently used commonly by the export companies and logistics companies through provision of various payment measures, support of foreign currency payment, etc. and security of reliability/system stability, etc. for the compatible payment with other systems as the prerequisite for the successful settlement of the auxiliary costs EPS. It is expected that satisfaction of the uTradeHub users such as export/import companies and logistics companies will be increased, user-oriented customized information services such as raw cost prediction service through calculation of auxiliary costs could be available in the future and efficiency of work processes related to auxiliary costs will be increased, by providing the EPS through various single window based payment measures through establishment of the export/import auxiliary costs payment system.