The invention discloses a processing method of a functional beverage of whole litchi with shells. The processing method comprises the following technological steps of performing cleaning on whole litchi, performing cutting, performing kernel removal, performing enzyme addition, performing ultrasonic pressing, performing suction filtration, performing microfiltration, performing ultrafiltration, performing concentration, performing blending, performing pulse electric field sterilization and the like. The functional litchi beverage prepared by the method not only is high in nutritional and health care value, but also is better in sensory evaluation effects.