Through the numerical simulation technology, a medical blister packaging containers thermoforming, based on sheet thickness variation and distribution at various points, was simulated during the plug-assisted thermoforming process, verifying the reliability of the finite element simulation methods. The simulation presenting vessel wall thickness distribution of the stretching core at different pre-stretching depth was also conducted, finding out the best pre-stretching depth contributing to more uniform values of thickness distribution, resulting in optimization of process parameters. The finite element model was established using SolidWorks software, and Ansys Polyflow software was applied for the simulation of the thermoforming process of medical blister packaging container. Through the experimental study of thermoforming on the actual molding products, the reliability of finite element simulation results was verified. The relative error of the results between the simulation value and test value was about 2%, representing that the simulation results was in accordance with the actual situation, and the simulation was quite reliable. Through the finite element simulation for the medical blister packaging products, the results were verified that the best pre-stretching depth value of this thermoforming was 6.5 mm.