The structural isomerism of the covalent organic framework (COF) has a significant effect on the electrochemiluminescence (ECL) performance. Herein, we report a pair of isomeric COFs, (TFPB-BD(OMe)2-H and TAPB-BD(OMe)2-H), based on the different directions of imine linkages and further conversion of the imine to the quinoline structure. The obtained two isomeric COFs with the same composition and similar structures exhibit dramatic differences in the photoelectrochemical and ECL fields. Indeed, TFPB-BD(OMe)2-H demonstrates robust ECL emission superior to that of TAPB-BD(OMe)2-H. The difference in ECL performance is due to the stronger polar interaction of TFPB-BD(OMe)2-H than that of TAPB-BD(OMe)2-H. The polarity is derived from the uneven charge distribution within the framework and enhances the electron interactions. In addition, the ordered conjugate skeleton provides high-speed charge transport channels for carrier transport. Therefore, the TFPB-BD(OMe)2-H presents a smaller band gap energy and stronger polarization interaction, which are more favorable to charge migration to achieve stronger ECL signals. Furthermore, we describe a convenient ECL sensor for detecting toxic As(V) with an outstanding detection property and ultralow detection limit. This work provides a guiding principle for the design and development of ECL organic luminophores.