Halogen atoms possess distinct atomic polarizabilities and have been recently employed in molecular junctions composed of saturated alkanethiol to greatly enhancing tunneling currents, dielectric responses, and plasmonic properties. However, their influence in fully conjugated molecular systems remains insufficiently understood. Here, a series of conjugated molecules, HSCH₂TPDA-X (X = H, F, Cl, Br, I), based on the fully conjugated triphenyldiacetylene (TPDA, C₆H₄C≡CC₆H₄C≡CC₆H₄) backbone were designed, and Metal (Ag/Au)-SAMs//Eutectic gallium-indium alloy (EGaIn) molecular junctions were constructed to systematically investigate how halogen substitution affects charge transport in conjugated systems. The J–V characteristics of the HSCH₂TPDA-X molecules remain stable over the measured temperature range, exhibiting temperature-independent behavior that indicates a tunneling-dominated charge transport mechanism. Single-level model (SLM) fitting reveals that halogen substitution (X = H, F, Cl, Br, I) does not significantly alter the highest occupied molecular orbital (HOMO)–Fermi level alignment, while the coupling strength is positively correlated with the current density. Density-functional theory (DFT) density-of-states (DOS) analysis reveals that, despite local terminal orbital shifts induced by halogen substitution, the overall DOS of the metal–self-assembled monolayer (SAM) closely follows that of the TPDA π-backbone, indicating a π-conjugated backbone pinning effect that constrains halogen-induced perturbations. These results contrast with previous saturated systems and indicate an observation of strong π-backbone pinning effect in conjugated system.