Farm-to-door online retail for fruit and vegetable is new business mode in China, which could connect farmers and customers directly. This mode is a promising business field as it could offer fresh and convenient agri-food to citizens, who barely have time to go to food markets on weekdays. However, with the growing of customer's amount, the efficiency of warehouse and logistics operations has been the block of its expansion. And currently the most time-consuming procedures in Delivery Centre (DC) are order picking and goods delivery, which are conducted one after another. In order to improve the operation efficiency of DC, we proposed a group-based order batching method to organize the warehouse and delivery operations as a pipeline. Firstly, the order picking process is modelled, which refers to vehicle routing plan. Then, we employ the group technology and put forward a group-based order batching method. Finally, we apply the proposed methodology on the farm-to-door fruit and vegetable online retail company in China. The result shows that the group-based order batching method could greatly reduce the operation time. This is a new order batching method, which could promote the development of farm-to-door business mode for fresh agri-food in China. And it is also offer a new idea for order picking process of large B2C online retailers.