The wrinkles are pervasive in ultrathin two-dimensional (2D) materials, but the regulation of wrinkles is rarely explored systematically. Here, we employed a series of carboxylic acids (from formic acid to octanoic acid) to control the wrinkles of Zr-BTB (BTB=1, 3, 5-(4-carboxylphenyl)-benzene) metal-organic framework (MOF) nanosheet. The wrinkles at the micrometer scale were observed with transmission electron microscopy. Furthermore, high-angle annular dark-field (HAADF) images showed lattice distortion in many nanoscale regions, which was precisely matched to the nano-wrinkles. With the changes of hydrophilicity/hydrophobicity, MOF-MOF and MOF-solvent interactions were possibly synergistically regulated and wrinkles with different sizes were obtained, which was supported by HAADF, molecular dynamics, and density functional theory calculation. Different wrinkle sizes resulted in different pore sizes between the Zr-BTB nanosheet interlayers, providing highly-oriented thin films and the successive optimization of kinetic diffusion pathways, proved by grazing-incidence wide-angle X-ray scattering and nitrogen adsorption. The most suitable wrinkle pore from Zr-BTB-C4 exhibited highly efficient chromatographic separation of the substituted benzene isomers. Our work provides a rational route for the modulation of nanoscale wrinkles and their stacked pores of MOF nanosheets and improves the separation abilities of MOFs.