The invention provides a grafting method for fortunella margarita, and belongs to the field of agricultural planting. The method specifically includes the following steps: firstly, germination accelerating and seedling raising are performed by adopting seeds of poncirus trifoliata, the obtained seedlings are used as rootstocks of grafting of the fortunella margarita, and a biochemical fertilizer is added into field planting pits of the obtained rootstock seedlings, wherein the biological fertilizer is obtained by mixed fermentation of banana stalks, bagasse, peanut bran, sweet potato stems, chicken manure, activated sludge, Chinese gleditsia sinensis fruit extract, tea stem extract, an EM agent and an additive; and fortunella margarita scions are selected, when grafting is performed, an accelerator is sprayed, and reasonable field management is performed. The grafting method provided by the invention can improve the survival rate of the fortunella margarita grafted seedlings, save a fertilizer, improve a yield, prevent diseases, and is suitable for large-scale systematic planting, and can increase a yield and income for growers.