Constitutional isomerism of covalent organic frameworks (COFs) has recently garnered attention for its potential applications in advanced photoelectrochemical fields. However, there have been no reports of materials in which half of the linkages between building blocks of the COFs are isomerized (so-called semi-isomerism) as a means of modulating the physicochemical properties of COFs. In this work, semi-isomeric pyrene-based COFs with the same topology were synthesized with imine linkages, namely, Py-Py and SI-Py COFs. Both COFs featured different imine orientations in half of the linkages. Tiny atomic-level dislocations of the imine linkages led to different electron orbital contributions and bandgaps (2.39 vs 2.44 eV for the Py-Py COFs and SI-Py COFs, respectively), resulting in distinct electron transfer and photoelectrochemical properties. In comparison with the Py-Py COFs, the SI-Py COFs with imine semi-isomeric linkages exhibited superior electrochromic performance over the optical modulation range (35% vs 24%), response time (0.29/2.1 s vs 0.72/3.8 s), and coloration efficiency (180 vs 144 C cm −2 ).