This paper presents an impedance model of on-chip power distribution network (PDN), which is an efficient criterion for estimating simultaneous switching noises (SSNs) on 3-D integrated circuit (IC). The impedance of on-chip PDN, including the effect of silicon substrate, is accurately modeled based on partial element equivalent circuit (PEEC) and layered Green's function (LGF). The equivalent circuit model of PDN is extracted based on the physical dimensions and electrical material characteristic of PDN at first. And then the LGF is used to consider the effect of silicon substrate for improving the accuracy of on-chip PDN impedance model. The effectiveness of proposed model has been validated by full wave simulation. The high order resonance of PDN impedance can also be accurately predicted.