The invention belongs to the technical field of plant breeding, and in particular relates to a single flower selfing isolation method for small chili. The method comprises the following steps: (1) selecting an excellent single plant, namely in the flowering period, selecting the excellent single plant according to a breeding objective, and marking; (2) preparing a capsule shell, namely separating a shell cap from a shell body of a hollow hard capsule shell; (3) selecting a flower bud, namely selecting a large flower bud which is expected to bloom in the next day; (4) treating the flower bud, namely holding the flower bud to be treated by one hand, holding the capsule shell, which is matched with the flower bud in size, by the other hand, slightly sleeving the flower bud with the lower opening of the capsule shell over the widest part of the flower bud, and marking a flower stalk; (5) managing after the treatment in a method which is the same as a conventional field management method for the production of small chili. The capsule shell used in the method is low in cost and does not hurt the flower bud and the flower stalk when being used, the operation is convenient and easy, and the work efficiency is high; moreover, the capsule shell with certain elasticity and permeability does not influence the cracking of anther and pollination, and thus the selfing setting rate of the small chili is high.