The mutation described by non-instantaneous pulses will stay in a limited time interval. This phenomenon is common in clinical medicine, bioengineering, chemistry, physics and other fields. In order to reflect the change law of things more profoundly and accurately, the existence and uniqueness of solutions for a class of boundary value problems of fractional differential equations with non-instantaneous impulses were studied. The operator was defined by establishing an integral equation equivalent to the boundary value problem, and its complete continuity was proved. By using Schauder fixed point theorem, the sufficient conditions for the existence of solutions of the boundary value problems were obtained. The uniqueness theorem of solutions was obtained by using the contraction mapping principle.