Experimental investigations and density functional theory (DFT) calculations were carried out to study the comprehensive effect of different 3,5-heptanedioldibenzoate (HDDB) optical isomers as the internal electron donor on the catalytic performance of Ziegler−Natta catalysts. The experimental catalytic activity of HDDB has a positive correlation with the relative content of the mesomer incorporated during catalyst preparation, while the hydrogen response of HDDB displayed a negative correlation with the relative content of the mesomer. In order to apply the DFT calculation results to the macroscopic activity of the catalyst, the content of the active centers of the catalyst was analyzed. Assuming that the content of the active centers is proportional to the internal electron donor content of the catalyst, binary linear regression was carried out, which showed a good linear correlation between experimental activity data and internal electron donor content. Furthermore, the fitted activity of the single active centers aligned well with the calculated activation energies. These results revealed that the catalytic activity of polypropylene (PP) catalysts is dependent on both the active center content and the catalytic activity of an individual active center. Additionally, the lower hydrogen response of HDDB leads to a higher molecular weight of polypropylene obtained from the RS-containing catalyst compared to the SS-containing catalyst. Further study reveals that the hydrogen transfer reactions of 2,4-pentanediol dibenzoate (PDDB)/HDDB are influenced by the orientation of the methyl/ethyl groups in different isomers, which affect the activation energy differences between the hydrogen transfer reaction and the propylene insertion reaction, and finally influence the molecular weight of PP.