Two Co‐based supramolecular isomers were synthesized from a fluorinated carboxylic acid ligand under hydrothermal conditions at varying temperatures. Both exhibited similar one‐dimensional chain structures while different bending connections of the aromatic rings led to different supramolecular structures, namely CoCP‐1 and CoCP‐2, respectively. The structural differences of two isomers resulted in discrepant performance with regards to luminescence sensing and catalysis. CoCP‐1 demonstrated more significant luminescence quenching activity toward biomarkers 2,6‐dipyridinoic acid (DPA) and high vanilloid acid (HVA), which could be distinguished in the presence of Eu3+. The limit of detection (LOD) was found to be as low as 3.4 and 1.3 μM, respectively. The recovery rate of for HVA and DPA was within the range of 89.6‐101.2% and 99.7‐117.9% in simulated urine and serum, respectively, indicating potential reliability in monitoring these two analytes in real samples. Notably, CoCP‐2 exhibited catalytic activity for the oxidation of thioethers to sulfoxides. Our finding here suggests that the coordination conformation of the ligands within supramolecular isomers plays a pivotal role in determining the structure and luminescence sensing/catalysis performance.