Capillary discharge based pulsed plasma thrusters have great prospects of applications in in-orbit maneuvering of micro-nano satellites. In this paper, the influence of different capillary cavity structure parameters on the thruster's energy deposition process, ablation characteristics, output thrust parameters and plasma plume parameters under an energy level of 5 J were studied. The experimental results indicate that the increase of the inner diameter of the capillary cavity will significantly reduce the discharge current density, which leads the deposition energy and equivalent power to decrease; the increase of the cavity length helps to improve the energy transfer efficiency. The influence of cavity structure on the ablation characteristics is reflected in the influence of deposition energy per unit area on the tube wall temperature. When the inner diameter of the capillary increases from 1 mm to 3 mm, the ablation mass decreases significantly, and then the equivalent ablation mass remains approximately unchanged as the inner diameter of the cavity increases further; the ablation mass continues to increase as the capillary length increases, while the ablation mass per unit area continues to decrease. The impulse bit depends on the ablation mass and plasma plume velocity, and the difference in ablation characteristic further affects the plasma in the cavity. The density and equivalent pressure determine the plasma electrothermal acceleration process. The continuous increase in the diameter and length of the capillary cavity will induce the acceleration process to lag behind the discharge and ablation process. And the decrease of the deposited energy impedes the electrothermal acceleration process, which results in the decrease of the impulse bit, specific impulse, and the overall efficiency. Furthermore, the overall efficiency transfer model analysis indicates the influence of the capillary inner diameter on thruster efficiency is mainly reflected in the energy transfer efficiency, and the capillary length change mainly affects the electrothermal acceleration efficiency. The overall efficiency optimization of the thruster needs to start from increasing both energy deposition efficiency and acceleration efficiency.