We investigate the process of pulsed laser cooling using a self-constructed molecular dynamics simulation (MD-Simulation) program.We simulate the Doppler cooling process and pulsed laser Doppler cooling process of a single 40Ca+ion,and the comparison with the experimental results shows that this self-constructed MD-Simulation program works well in the weak laser intensity situation.Furthermore,we analyze the pulsed laser Doppler cooling process of a single 27A1+ion.This program can be used to analyze the molecular dynamic process of various situations of Doppler cooling in an ion trap,which could give predictions and experimental guidance.