This study conducts a three-dimensional electro-thermal time-domain simulation for numerical analysis of cylindrical-shaped phase change memories (PCMs). The influence of chalcogenide material, germanium antimony telluride (GeSbTe or GST), structure on PCM operation is explored. GST with vertical structure exhibits promising characteristics. The bottom electrode contact (BEC) is advanced to improve the operation of PCMs, where a 25% reduction of the required programming current is achieved at a cost of 26% reduced resistance ratio. The position of the BEC is then shifted to further improve the performance of PCMs. The required programming current is reduced by a factor of 11, where the resistance ratio is only decreased by 6.9%. However, the PCMs with a larger shift of BEC are sensitive to process variation. To design PCMs with less than 10% programming current variation, PCMs with shifted BEC, where the shifted distance is equal to 1.5 times the BEC's radius, is worth considering. This study quantitatively estimates the structure effect on the phase transition of PCMs and physically provides an insight into the design and technology of PCMs.