MFI and MWW zeolite nanosheets are building units for state-of-the-art zeolite thin films for gas separation. In this study, the structures of exfoliated MFI and MWW zeolite nanosheets were determined using a combination of experimental and simulation methods. Based on characterization results from atomic force microscopy and transmission electron microscopy, the structures and thicknesses of the exfoliated zeolite nanosheets were proposed. After optimization with Car-Parrinello molecular dynamics, X-ray diffraction patterns and electron diffraction patterns are simulated from these structures. The agreement between experimental and simulated characterization data suggested that the proposed structures should represent the actual structures of the exfoliated zeolite nanosheets. The methods used in this study can be extended to determining structures of other zeolite nanostructures.