A robust simulation framework was developed for nanoscale phase change memory (PCM) cells. Starting from the reaction rate theory, the dynamic nucleation was simulated to capture the evolution of the cluster population. To accommodate the non-uniform critical sizes of nuclei due to the non-isothermal conditions during PCM cell programming, an improved crystallization model was proposed that goes beyond the classical nucleation and growth model. With the above, the incubation period in which the cluster distributions reached their equilibrium was captured beyond the capability of simulations with a steady-state nucleation rate. The implications of the developed simulation method are discussed regarding PCM fast SET programming and retention. This work provides the possibility for further improvement of PCM and integration with CMOS technology.