In order to study the effects of the heat setting temperature of modified Polyester (PET) film on its performance, the structure, crystallinity and the thermal effect of two kinds of PET film were tested and evaluated. The results showed that after heat setting with different temperatures, the chemical composition of two kinds of PET film did not change but with the change in crystallinity states. As heat-setting temperature went up, modified PET film’s crystallinity decreased. Improving heat setting temperature had little effect on the Tg and melting point of the resin, and as heat-setting temperature went up, cooling crystallization peak temperature shifted to higher temperature. Increasing heat setting temperature helped to suppress the secondary crystallization ability of BOPET.