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We first optimize culture conditions to generate more reproducible HIOs with predictable growth in phototunable poly (ethylene glycol)-based hydrogels, and then systematically investigate the role of light-mediated matrix softening in guiding crypt formation. The light dose delivered to crypt-sized regions adjacent to growing organoids is a key factor in maintaining organoid cell viability, as well as crypt budding and elongation. With optimized light doses, predictable epithelial shape changes result in programmable crypt formation, confirmed by the presence of proliferative (Ki67+) and niche-defining Paneth (Lyz+) cells. This methodology could be readily adopted for other budding and branching organoids to facilitate controllable changes in morphogenesis or cell migration. 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