The severe situation caused by THE COVID-19 epidemic has not only hindered the steady development of social economy, but also had a great impact on the development of e-commerce logistics. For e-commerce enterprises, logistics cost is an important factor that affects the operation effect and consumer experience. Based on this, this study proposes cost control methods for e-commerce logistics in the prevention and control of COVID-19 environment. In this study, based on the actual environment of COVID-19 prevention and control, the logistics cost algorithm during the epidemic period is designed on the basis of the analysis of the influencing factors of e-commerce logistics cost, and the cross-border logistics strategy that conforms to the background of COVID-19 prevention and control and the demand of e-commerce logistics cost control is developed to better reduce the operating cost of logistics enterprises. The e-commerce logistics cost control method proposed in this article is effective in the prevention and control of new crown pneumonia, and the overall actual cost is within the budgeted cost range. The experimental results prove that the e-commerce logistics cost control method designed in this paper can help e-commerce companies achieve good economic benefits and proves that it has higher application advantages.