To analyze the trap depth and ion heating rate of a surface ion trap under the influence of substrate power loss and voltage loss, in this paper we proposes analytic expressions of trap depth and ion heating rate. The results show that the voltage loss of Si substrate can reduce the trap depth by 17.19%, and the power loss would accelerate the ion heating rate by 13.37%. In order to reduce the influence of substrate effect, a new surface ion trap with low self-heating and voltage-loss is proposed in this paper, whose substrate is insulated by some vacuum trench to reduce the equivalent conductivity and capacitance. The simulation results illuminate that compared with the surface ion trap with normal Si-SiO2 substrate, the one with vacuum trench insulation exhibits a 20.22% increase in trap depth and a 54.44% reduction in power loss.