The SiC metal-oxide-semiconductor field effect transistor (MOSFET), as a third-generation wide-bandgap semiconductor, possesses advantages such as low on-resistance, high power density, fast switching speed, and low switching losses, making it a promising candidate in aerospace equipment. However, electrons in space can cause total ionizing dose (TID) effects, leading to the performance degradation of electronic components, especially in deep space environments with high-energy and high-flux electron irradiation. In this study, electron irradiation induced TID effects were experimentally investigated in SiC MOSFETs with different structures of double trench (DT) and asymmetric trench (AT). The DT-MOSFET was found to be more sensitive to TID effects. Furthermore, the technology computer aided design (TCAD) simulation was performed to reveal the mechanism of the trench structure dependent TID effects. It was revealed that compared to DT-MOSFET, the semi-enclosed P+ well structure in the AT-MOSFET provides protection to the bottom of the gate oxide layer, reducing the electric field intensity in that region and suppressing the impact of TID effects.