System dynamics provides a more intuitive and effective tool for system analysis in area supply chain logistics. By using method of system dynamics, this paper builds up a 3PL-HUB three echelon supply chain system from the perspective of costs, compares supply chain logistics costs variation in two cases with and without 3PL-HUB involved in, simulates logistics costs of each node enterprise, and fully analyzes the influence of 3PL-HUB on bullwhip effect and fluctuation of inventory of supply chain members. It shows that 3PL-HUB can reduce costs and benefit all the enterprises of whole supply chain, which represents a method to enhance supply chain synergy.