In order to study the influence of three-grid assembly thermal deformation caused by heat accumulation on breakdown times and an ion extraction process, a hot gap test and a breakdown time test are carried out to obtain thermal deformation of the grids when the thruster is in 5 kW operation mode. Meanwhile, the fluid simulation method and particle-in-cell-Monte Carlo collision (PIC-MCC) method are adopted to simulate the ion extraction process according to the previous test results. The numerical calculation results are verified by the ion thruster performance test. The results show that after about 1.2 h operation, the hot gap between the screen grid and the accelerator grid reduce to 0.25-0.3 mm, while the hot gap between the accelerator grid and the decelerator grid increase from 1 mm to about 1.4 mm when the grids reach thermal equilibrium, and the hot gap is almost unchanged. In addition, the breakdown times experiment shows that 0.26 mm is the minimal safe hot gap for the grid assembly as the breakdown times improves significantly when the gap is smaller than this value. Fluid simulation results show that the plasma density of the screen grid is in the range 6×10 17-6×10 18 m 13 and displays a parabolic characteristic, while the electron temperature gradually increases along the axial direction. The PIC-MCC results show that the current falling of an ion beam through a single aperture is significant. Meanwhile, the intercepted current of the accelerator grid and the decelerator grid both increase with the change in the hot gap. The ion beam current has optimal perveance status without thermal deformation, and the intercepted current of the accelerator grid and the decelerator grid are 3.65 mA and 6.26 mA, respectively. Furthermore, under the effect of thermal deformation, the ion beam current has over-perveance status, and the intercepted current of the accelerator grid and the decelerator grid are 10.46 mA and 18.24 mA, respectively. Performance test results indicate that the breakdown times increase obviously. The intercepted current of the accelerator grid and the decelerator grid increases to 13 mA and 16.5 mA, respectively, due to the change in the hot gap after 1.5 h operation. The numerical calculation results are well consistent with performance test results, and the error comes mainly from the test uncertainty of the hot gap.