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. In this work, we propose reconfigurable skyrmion-based logic gates with auto-annihilating skyrmion function, and six logical operations can be implemented in our model relying on the competition among the spin transfer torque (STT), skyrmion Hall effect (SkHE), skyrmion-edge repulsion, skyrmion-skyrmion topological repulsion, and voltage-controlled magnetic anisotropy (VCMA) effect. The influence of temperature on the logical operation processes indicates that the temperature range for achieving all types of logic operations and automatic annihilation function is 0–96 K. The function of automatically clearing skyrmions after the completion of logic operations can free up space for storing unnecessary skyrmions, and save energy consumption for applying additional current to eliminate them. Our results can be beneficial for the design and development of magnetic skyrmion logic gates.