Two-dimensional (2D) materials are known for their potential to exhibit anisotropic transport properties due to their layered structures. However, the anisotropic ion conduction of 2D metal-organic frameworks (MOFs) has been rarely explored. In this study, we investigated the anisotropic proton conduction along the in-plane and stacking directions of two analogs of undulating 2D MOFs: [Mn(salen)]2[Pt(CN)4]·H2O (MnPt) and [Mn(salen)]2[PtI2(CN)4]·H2O (MnPtI). This investigation was conducted using both experimental methods, involving single crystals, and theoretical calculations. Compared to the relatively isotropic proton conduction of MnPt at 85 °C and 95% relative humidity (RH), with a stacking direction conductivity (σstacking) of 1.8 × 10-5 S/cm, which is approximately 2.9 times the in-plane conductivity (σin-plane), MnPtI exhibited highly anisotropic proton conduction. The σstacking of MnPtI under the same conditions (85 °C, 95% RH) was 1.5 × 10-4 S/cm, which is 83 times higher than its σin-plane. Additionally, the activation energy for proton conduction in MnPtI ranged from 0.65 to 0.73 eV, which is higher than the 0.48 eV observed for MnPt. Theoretical calculations confirmed that slight differences in local structures, including node distortions between MnPt and MnPtI, significantly influenced the activation energies for water migration. This was attributed to the formation of hydrogen bonds between layers and water molecules.