In order to investigate the molecular evolution mechanism of polymer chains during packing and cooling stage, a PP model which contains 8 chains with polymerization degree of 2000 was constructed. Based on molecular dynamics theory, the transient structure of polymer chains and its evolution law were studied. The results show that no matter shearing flow or packing and cooling, the bond length and bond angle of polymer chains don’t get changed, what changed only is the aggregation and motion state. The change of potential energy indicates that the molecular chains tend to a low energy state due to its disorientating during packing and cooling, and meanwhile, the radius of gyration and mean square displacement results suggest that polymer chains don’t migrate but only elastically recover at the end shearing position. Moreover, the higher shear rate flow which molecular chains experience, the greater the degree of elastic recovery during packing and cooling process.