Performance optimization associated with optical modulators requires reasonably accurate predictive models for key figures of merit. Interleaved PN-junction topology offers the maximum mode/junction overlap and is the most efficient modulator in depletion-mode of operation. Due to its structure, the accurate modelling process must be fully three-dimensional, which is a nontrivial computational problem. This paper presents a rigorous 3D model for the modulation efficiency of silicon-on-insulator interleaved junction optical phase modulators with submicron dimensions. Solution of Drift-Diffusion and Poisson equations were carried out on 3D finite-element-mesh and Maxwell equations were solved using Finite-Difference-Time-Domain (FDTD) method on 3D Yee-cells. Whole of the modelling process has been detailed and all the coefficients required in the model are presented. Model validation suggests < 10% RMS error.