This paper presents dual-layer proton irradiation profile to improve the thermal stability of high-resistivity substrate formed by low-fluence proton irradiation. Dual-layer irradiation uses targeted irradiation to the Si-SiO2 interface to reduce the fluence required for preventing the formation of conduction layer after annealing. Thermal stability of effective substrate resistivity is evaluated indirectly through inductor Q-factor measurement before and after annealing at 260°C for 1-minute. With the same total fluence of $4\times 10^{14}\text{cm}^{-2}$, measurement result shows dual-layer irradiation profile can suppress post-anneal Q-factor degradation from 17% in conventional proton irradiation to 1%. The required active devices margin from irradiated area is reduced by 26% to $22\mu \mathrm{m}$, compared to $30\mu \mathrm{m}$ in conventional irradiation.