Heavy metal ions and antibiotic contamination have become a major environmental concern worldwide. The development of efficient recognition strategies of these pollutants at ultra‐low concentrations in aqueous solutions as well as the elucidation of the intrinsic sensing mechanism are challenging tasks. In this work, unique luminescent Ln‐MOF materials (NIIC‐3‐Ln) were assembled by rational ligand design. Among them, NIIC‐3‐Tb demonstrated highly selective luminescence quenching response toward Hg2+ and sulfadiazine (SDI) at subnanomolar concentrations in less than 7 s. In addition, a Hg2+ sensing mechanism through chelation was proposed on the basis of single‐crystal X‐ray diffraction analysis and Hg2+ adsorption study. The interaction mechanism of NIIC‐3‐Tb with SDI was revealed using a newly developed approach involving a (TD‐)DFT based quantification of the charge transfer of a MOF‐analyte supramolecular complex model in the ground and excited states. Effect of ultrasonic treatment on the surface morphology important for MOF sensing performance was revealed by gas adsorption experiments. The presented results indicate that NIIC‐3‐Ln is not only an advanced sensing material for the efficient detection of Hg2+ and SDI at ultra‐low concentrations, but also opens up a new approach to study the sensing mechanism at the molecular level at ultra‐low concentrations.