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Structural and compositional inhomogeneity is common in zeolites and considerably affects their properties. Thickness-limited lateral resolution, lack of depth resolution, and electron dose-constrained focusing limit local structural studies of zeolites in conventional transmission electron microscopy (TEM). We demonstrate that a multislice ptychography method based on four-dimensional scanning TEM (4D-STEM) data can overcome these limitations. Images obtained from a ~40-nanometer-thick MFI zeolite exhibited a lateral resolution of ~0.85 angstrom that enabled the identification of individual framework oxygen (O) atoms and the precise determination of the orientations of adsorbed molecules. Furthermore, a depth resolution of ~6.6 nanometers allowed probing of the three-dimensional distribution of O vacancies, as well as the phase boundaries in intergrown MFI and MEL zeolites. The 4D-STEM ptychography can be generally applied to other materials with similar high electron-beam sensitivity.