Localization of multiple hydrogels is expected to develop the structure of 3D tissue models in a location specific manner. Here, we successfully localize morphogenesis within individual tissues by exposing different hydrogel conditions to different parts of the tissues. We develop a unit-based scaffold with a unique frame design to trap hydrogel solutions inside their designated units. Interestingly, this unit-based scaffold within an optimal range of dimensional size and surface wettability can trap several cubic millimeters of hydrogels. This localization capability enables the spatial organization of hydrogel compositions, growth factors and physical conditions, as well as the position of biological samples (cells, spheroids, reconstituted tissues) relative to each hydrogel compartment. We succeed to localize the branching development of reconstituted human epithelial tissues according to the localized biomolecular and physical cues from hydrogels, regardless of the initial tissue configurations. Unlike 3D-bioprinting or microfluidics, the localization with this unit-based scaffold requires only manual pipetting and handling without any specialized equipment or skills, thus ready to use by researchers from any field. This scaffold-based localization provides a new promising route to spatially control morphogenesis, differentiation, and other developmental processes within organoids or other 3D tissues, resulting in 3D functional models for practical biomedical applications.