Chirality amplification and transfer strategies enable covalent organic polymers (COPs) to adopt supramolecular helicity with diverse structural and functional possibilities. Although helicity and chiroptical response typically correlate, we reveal a distinct chiroptical isomerization in helical COPs, where polymers with identical mesoscopic helicity exhibit opposite chiroptical activities. Using a supramolecular templating method, we prepared helical polyimines that maintain uniform helicity yet display reversed Cotton effects upon subtle variations in a single polymerization parameter, such as monomer structures, good-solvent identity, or good/poor solvent ratios. This inversion likely originates from opposite chiral packing of sub-nanometer building units while preserving overall helicity. Leveraging the high symmetry and dynamic covalency of these polyimines, we transformed them into thermodynamically stable helical covalent organic frameworks (COFs) via stepwise linker exchange. Remarkably, both the mesoscopic helicity and the chiroptical isomerization behavior were retained throughout the crystallization process, providing direct evidence for chiroptical isomerization in COFs and enabling advanced design principles for tunable chiral materials.