A method for manufacturing a honeycomb structure, the honeycomb structure comprising: porous partition walls via which a plurality of cells constituting through channels for a fluid are partitioned; and an outer peripheral wall positioned in the outermost periphery of the structure, open frontal areas of predetermined cells in an end face of the structure on a fluid inlet side thereof and open frontal areas of remaining cells in an end face of the structure on a fluid outlet side thereof being provided with plugged portions, wherein the outward end faces of the plugged portions are flat, the plugged portions do not have any bubble having a diameter of 0.3 mm or more, and a value obtained by dividing the standard deviation of the plugging depths of the plugged portions by the average plugging depth of the plugged portions is 0.15 or less, the method comprising: a masking process of attaching a sheet to one end face of a formed honeycomb article comprising porous partition walls via which a plurality of cells constituting through channels for a fluid are partitioned and an outer peripheral wall positioned in the outermost periphery of the article, and making holes in the positions of the sheet superimposed on the cells in which plugged portions are to be formed; a first press-in process of pressing the end of the formed honeycomb article, to which the sheet is attached, into a container in which a plugging material is received, to press the plugging material into the cells via the one end face of the formed honeycomb article through the holes formed in the sheet; and a second press-in process of moving, along the surface of the sheet, a press-in jig including a pressurization member having a hardness of 60 to 90 degrees, having a plate-like shape chamfered along one side of the shape perpendicular to a thickness direction and having a flat face disposed adjacent to the chamfered face in parallel with the thickness direction, in a state where the angle (θ1) between a pressurization face, which is the chamfered face, and the sheet is from 15 to 50°, and where, when the pressurization member tilt angle (θ3), which is the angle of the angle of the pressurization member tilted so as to fall down along a direction in which the press-in face is formed, is 0°, the press-in jig is moved along the surface of the sheet (21 in a state where the flat face comes into contact with the sheet to press, by the pressurization face, the plugging material supplied between the sheet and the pressurization face into the cells in which the plugging material is charged, over the plugging material, through the holes formed in the sheet. a masking process of attaching a sheet to one end face of a formed honeycomb article comprising porous partition walls via which a plurality of cells constituting through channels for a fluid are partitioned and an outer peripheral wall positioned in the outermost periphery of the article, and making holes in the positions of the sheet superimposed on the cells in which plugged portions are to be formed; a first press-in process of pressing the end of the formed honeycomb article, to which the sheet is attached, into a container in which a plugging material is received, to press the plugging material into the cells via the one end face of the formed honeycomb article through the holes formed in the sheet; and a second press-in process of moving, along the surface of the sheet, a press-in jig including a pressurization member having a hardness of 60 to 90 degrees, having a plate-like shape chamfered along one side of the shape perpendicular to a thickness direction and having a flat face disposed adjacent to the chamfered face in parallel with the thickness direction, in a state where the angle (θ1) between a pressurization face, which is the chamfered face, and the sheet is from 15 to 50°, and where, when the pressurization member tilt angle (θ3), which is the angle of the angle of the pressurization member tilted so as to fall down along a direction in which the press-in face is formed, is 0°, the press-in jig is moved along the surface of the sheet (21 in a state where the flat face comes into contact with the sheet to press, by the pressurization face, the plugging material supplied between the sheet and the pressurization face into the cells in which the plugging material is charged, over the plugging material, through the holes formed in the sheet.