Sub-angstrom resolution imaging of porous materials like zeolites is important to reveal their structure-property relationships involved in ion exchange, molecule adsorption and separation, and catalysis. Using multislice electron ptychography, we successfully measured the atomic structure of zeolite at sub-angstrom lateral resolution for 100-nanometer-thick samples. Both lateral and depth deformations of the straight channels are mapped, showing the three-dimensional structural inhomogeneity and flexibility. Since most zeolites in industrial applications are usually tens to hundreds of nanometers thick, the sub-angstrom resolution imaging and accurate measurements of depth-dependent local structures with electron ptychography at low-dose condition will find wide applications in porous materials close to their industrially relevant conditions.