A method of manufacturing a plugged honeycomb structure has a plugging process which includes the steps of: immersing one end (a first end) of a honeycomb base material in a plugging slurry while vibrating the plugging slurry; after bringing an internal part of a cell into a negative pressure and then returning it into an atmospheric pressure, vibrating the plugging slurry to make the plugging slurry enter a first open end of the cell; and drying the plugging slurry having entered the first open end of the cell to form a first plugging portion at the first end.