Exploring the molecular-level interaction mechanisms between the molecular structure and conformation to develop efficient nucleating agents is an intriguing endeavor. In this study, we synthesized a series of indole acid derivative organic metal salt biobased nucleating agents with different numbers of methylene linkages for the preparation of PLA and zinc salts of indolic acid composite materials (PLA-IA-Zn). The results demonstrated that 3-indolecarboxylic acid zinc salt (ICA-Zn) without methylene linkages exhibited excellent nucleating activity. With an addition level of 0.5 wt %, PLA-ICA-Zn exhibited increased crystallization peak temperature and crystallinity to 117.5 °C and 54.9%, respectively, while the half-crystallization time was reduced to 2.6 min at 135 °C. Time-resolved Fourier transform infrared spectroscopy and molecular dynamics results demonstrate that the absence of methylene connectivity significantly enhances the van der Waals energy between the nucleating agent and PLA in the molten state, promoting intermolecular and intramolecular interactions within PLA, increasing the content of the gt conformation (corresponding to the 10 3 helical conformation of the α-type PLA crystal) during the PLA crystallization process, and thereby reducing the nucleation barrier. The antibacterial results showed that the PLA-IA-Zn composite materials achieved inhibition rates of over 93.2% for Escherichia coli and over 87.3% for Staphylococcus aureus. This study provides a new strategy at the molecular level for designing efficient nucleating agent molecules with both antibacterial functionality and high performance.