Zeolites are among the most important heterogeneous catalysts, widely employed in separation reaction, fine chemical production, and petroleum refining. Through rational design of the frameworks, zeolites with versatile functions can be synthesized. Local imaging of zeolite structures at the atomic scale, including the basic framework atoms (Si, Al, and O) and extra-framework cations, is necessary to understand the structure-function relationship of zeolites. Herein, we implemented electron ptychography into direct imaging of local structures of two zeolites, Na-LTA and ZSM-5. Not only all the framework atoms but also extra-framework Na+ cations with only 1/4 occupation probabilities in Na-LTA were directly observed. Local structures of ZSM-5 zeolites having guest molecules among channels with different orientations were also unraveled using different reconstruction algorithms. The approach presented here provides a new way to locally image zeolites structure, and it is expected to be an essential key for further studying and tuning zeolites active sites at the atomic level.