Logistics runs through the entire process of an enterprise’s production and management. Logistics, as an enterprise’s" the third profit source", is an effective management tools for companies to obtain and maintain a competitive advantage, the management of logistics risk of marketing channels is a critical part of the risk management of channels. The paper introduces the logistics risk types, and from the systematic view, analyses the connotation of the logistics system of marketing channels, and factors influencing the logistics risk of marketing channels are indicated. On this base, a systematic dynamics model for the logistics risk of marketing channels is constructed, and the simulated results is obtained by Vensim PLE. The results show that it is essential for logistics risk management in marketing channel to control suppliers’, manufacturers’ and distributors’ own possible risks and decrease the outflow rate.