Fresh e-commerce is considered to be the next blue sea in the field of e-commerce, the market prospects are broad. However, at present, fresh e-commerce is still in the exploration stage of development, and due to the particularity of fresh products, there are many risks in its logistics operation, how to carry on the scientific appraisal and the prompt control to the related risk is the important question which faces at present. This paper analyzes the logistics operation risk of fresh e-commerce from four aspects of supply, circulation, service and external environment, and constructs the corresponding risk evaluation index system. Secondly, the risk evaluation model of fresh e-commerce logistics operation is constructed by using entropy method and grey clustering analysis method. Finally, the feasibility of the model is verified by an example analysis, and the corresponding risk prevention and control recommendations are put forward.