A method of manufacturing a honeycomb structure having honeycomb segments, which includes a masking step (S1) of attaching masking materials (8) to both end surfaces (2a) of the honeycomb segments (2), a stacked body bonding step (S2) of bonding the honeycomb stacked body (3) by bonding the plurality of honeycomb segments (2) together while interposing adhesive layers therebetween, an adhesive layer drying step (S3) of integrally fixing the honeycomb stacked body (3) by heating and drying the adhesive layers, a masking material separating step (S4), of separating the masking materials (8), and a grinding step (S5) of grinding an outer peripheral portion of the honeycomb stacked body (3) into a predetermined shape.