Novel chalcogenide-based phase change memory (PCM) is a promising candidate for next-generation non-volatile solid-state memory technology for its high resistance contrast, better endurance and writing speeds than flash memory. PCM cell stores data by a thermally induced phase transition between conductive poly crystalline (set) and resistive amorphous (reset) states, in a thin film of chalcogenide materials, such as GeSbTe (GST) alloy. Therefore, the determination of the maximum temperature of GST material is crucial in design and technology of PCM. In this study, a three-dimensional electro-thermal time-domain simulation is conducted for dynamic thermal analysis of the cylindrical PCMs, where the structure GST is a cone with different cone angle, ranging from 90° to 45°. Our preliminary result shows the relation between contact size of GST and required programming current for GST phase transition. The GST with 90° angle exhibits the smallest required programming current than the others. The angle and contact size of GST will modify the distribution of temperature and alters the maximum temperature of the GST material. This study quantitatively estimates the structure effect on phase transition of PCM and physically provides an insight into design and technology of PCMs.