With the rapid development of nanoelectromechanical system technologies, silicon nanostructures have attracted considerable attention for the remarkable mechanical properties. A number of studies have been made on the mechanical properties through theoretical analysis, atomistic or molecular dynamics and experiments. In this paper, the resonance frequency of the doping silicon nano-beam is investigated by a theoretical model based the semi-continuum approach to achieve the goal of accurately capturing the atomistic physics and retaining the efficiency of continuum model. The temperature dependence of the resonance frequency of the nanostructure is important for application design, which is considered by the Keating anharmonic model used to describe the strain energy at finite temperature. The resonance frequencies are also simulated by the molecular dynamics at different temperatures. The studies indicate that the resonance frequency of the P doped silicon nano-beam is influenced by the size, the doping concentration and the temperature. The results show that the resonant frequency decreases with the increase of the length of the beam, and increases with the increase of the doping concentration of the silicon nano-beam. The resonant frequency of silicon nano-beam decreases with the increase of temperature, but the changes of the resonant frequency is not obvious. The doping concentration has a little effect on the resonance frequency of the silicon nano-beam. The conclusion can be drawn that neither the effect of doping concentration nor the effect of temperature on resonant frequency of the silicon nano-beam is obvious, the size is a major factor influencing the resonance frequency of the silicon nano-beam.