The charge transport through supramolecular junctions exhibits unique quantum interference (QI) effects, which provide an opportunity for the design of supramolecular transistors. Benefiting from the configuration dependence of QI, configuration control of the supramolecular assemblies to demonstrate the QI features is a key but challenging step. In this work, we fabricated the supramolecular transistors and investigated the charge transport through the conducting channel of the individual π-stacked thiophene/phenylene co-oligomers (TPCOs) using the electrochemically gated scanning tunneling microscope break junction technique. We controlled the configuration of the supramolecular channel and switched the QI features between the anti-resonance and resonance states of the supramolecular channels. We observed the supramolecular transistor with its on/off ratio above 103 (∼1300), a high gating efficiency of ∼165 mV/dec, a low off-state leakage current of ∼30 pA, and the channel length scaled down to <2.0 nm. Density functional theory calculations suggested that the QI features in π-stacked TPCOs vary depending on the supramolecular architecture and can be manipulated efficiently by fine-tuning the supramolecular configurations. This work reveals the potential of the supramolecular channels for molecular electronics and provides a fundamental understanding of intermolecular charge transport.