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Hatchery is main that plays important role in aquaculture Sea urchin Tripneustes gratilla (Linnaeus 1758). The quality of Sea urchin egg is determined by the absorption of nutrients that carried throughout the gonad development while the quality of nutrients is very likely influenced by the type of food consuming. This research of substrate types on habitat breeding of Sea urchin embryonic development and larval morphometric had been done on October - November 2016 at the laboratory of marine aquaculture LIPI Center for Deep Sea Research. The Samples taken from three different habitats comprises Hative Besar, Liang and Suli. The purpose of this research is to determine the effects of substrates types on habitat breeding of Sea urchin embryonic development and larval morphometric. The method that has been used to determine the morphometric was done by measuring the diameter and height of the shell using a digital caliper and total body weight using a digital scale. To observe embryonic development and larval morphometric done by in vitro fertilization through eggs selection then cultured in petri dish at a density of 10 ind/ml. The result of this research is the most dominant quantity of embryonic development (72 hours) indicated by culture vessel from Hative Besar meanwhile the least is indicated by Liang. The greatest larval morphometric indicated by culture vessel from Hative Besar with length and height of larval body further the larval of culture vessel from Hative Besar shown ossification formation.