Novel chalcogenide-based phase change memories (PCMs) are known as one of next-generation non-volatile memory technologies for its high resistance contrast, better endurance and high writing speed. PCM cell stores data by a thermally induced phase transition between crystalline to amorphous states, and thus understanding of temperature distributes within a cell and determining the programming current of phase transition are crucial in design and technology of PCM. In this study, a three-dimensional electro-thermal time-domain simulation is conducted for dynamic analysis of the cylindrical-shaped PCMs. The structure GST is a cone with different cone angle, ranging from 90° to 45°. The relation between contact size of nanoscale GeSbTe (GST) alloy and the required programming current for phase transition is advanced. The preliminary result shows that the GST structure with a 90° angle exhibits the smallest required programming current, the fastest phase transition characteristic, the highest resistance contrast, and the best heat utilization efficiency. This study quantitatively estimates the structure effect on phase transition of PCM and physically provides an insight into design and technology of PCMs.