There is provided a honeycomb structure in which the structure is not segmented, or a smaller number of segments are integrated to suppress a local temperature rise and to reduce breakage by thermal stress at the time of use, and a method of manufacturing the structure. There is disclosed a honeycomb structure 1 comprising: a large number of cells 3 partitioned by cell walls 2 and extending through an axial direction. A flow channel separator 6 is formed in the honeycomb structure 1. There is disclosed a method of manufacturing the honeycomb structure 1 in which the flow channel separator 6 is formed by extrusion. There is disclosed a method of manufacturing the honeycomb structure 1 in which the flow channel separator 6 is formed by clogging.