Skyrmions are a spin texture with topological protection properties, which can be considered as an excellent candidate for the next generation of high-speed, nonvolatile, and low-power consumption spin devices due to their unique dynamic characteristics. However, in practical devices, skyrmions remain in the device after performing specific operations, resulting in unnecessary energy load on the device. In this work, we propose reconfigurable skyrmion-based logic gates with auto-annihilating skyrmion function, and six logical operationsamong the can be implemented in our model relying on the competitionspin transfer torque (STT), skyrmion Hall effect (SkHE), skyrmion-edgerepulsion, skyrmion-skyrmion topological repulsion, and voltage-controlled magneticanisotropy (VCMA) effect. The function of automatically annihilating skyrmions after executing logical operations is realized by utilizing the easy annihilation characteristic of skyrmions at the notch, which can greatly reduce the energy load of the system. Our results can be beneficial for the design and development of magnetic skyrmion logic gates.