Heterogeneous interfaces in most devices play a key role in the material performance. Exploring the atomic structure and electronic properties of metal-molecule interfaces is critical for various potential applications, such as surface sensing, molecular recognition, and molecular electronic devices. This study unveils a ubiquitous interfacial stereoelectronic effect in conjugated molecular junctions by combining first-principles simulation and scanning tunneling microscopy break junction technology. Single-molecule junctions with same-side interfacial anchoring (cis configuration) exhibit higher conductance than those with opposite-side interfacial anchoring (trans configuration). The cis and trans configurations can undergo reversible conversions, resulting in a conductance switching. The stability of these configurations can be adjusted by an electric field, achieving precise regulation of conductance states. Our findings provide important insights for designing high-quality materials and enhancing the device performance.