In this work, an anionic framework Co-MOF (1) was elaborately constructed, which underwent single-crystal-to-single-crystal (SC-SC) transformation to produce 1-Cr and 1-Fe after immersion in a CrCl3 or FeCl3 solution. Despite the similar crystal structure, the significantly enhanced proton conductivities of 1-Cr and 1-Fe far exceed that of 1 at all humidity and temperature conditions. Even at 30 °C and 98% RH, the proton conductivity of 1-Cr and 1-Fe can reach up to high values of 1.49 × 10–2 and 6.39 × 10–3 S cm–1, respectively, surpassing that of 1 by over 5000 times under identical conditions. The partial alteration of the proton-conducting carriers from metal-water cluster [Co(H2O)6]·6H2O] (1) to metal-hydroxyl-water clusters [Cr(OH)4(H2O)2]·6H2O] (1-Cr) and [Fe(OH)4(H2O)2]·6H2O] (1-Fe) can be attributed for the above-mentioned enhanced performance. The introduction of hydroxyl by SC-SC transformation can establish interconnected proton conduction pathways within the proton channels, which greatly facilitate proton conduction, affording much lower activation energies (0.12 eV for 1-Cr, 0.18 eV for 1-Fe, and 0.28 eV for 1). This research demonstrated that SC-SC transformation not only achieved significantly improved proton conduction but also contributed to a deeper understanding of the structure–property relationships, providing new insights into the design of advanced materials with enhanced proton conductivity.