A good understanding of the morphological and functional changes during early larval fish ontogeny is essential for the enhancement of larviculture techniques. This study applied an integrative approach to describe the ontogenetic development of the Japanese flounder (Paralichthys olivaceus) emphasizing the changes in histology and related functions of its digestive system. Changes in histological structures of the digestive tract, expression and activity of digestive enzymes (trypsin, chymotrypsin, lipase, pepsin, amylase), expression of energy metabolism (ATP synthase (atp), cytochrome-c-oxidase (cox), regulatory factors (neuropeptide Y (npy), cholecystokinin (cck)) and growth (insulin like growth factor 1 (igf1), growth hormone (GH)) were investigated and linked to larval biometrics. The larvae absorbed nutrients from its yolk upon hatching until mouth opening (3 DAH), before beginning its exogenous nutritional phase. The digestive tract differentiations were histologically observed at 5 DAH. The results showed that the targeted enzymes were genetically programmed and activated from hatching, except pepsin which was detected at 25 DAH coinciding with visible development of the gastric glands. The larval stages (3–5 DAH) were marked with high mortality at exogenous feeding transition and also at the onset of metamorphosis (20–30 DAH). Energy metabolism, growth and peptide regulatory factor related genes were transcribed and translated at hatching to assist upon the onset of exogenous feeding. Less feeding and growth delay were noticed between 20 and 30 DAH. The digestive system was fully developed by 35 DAH and larvae transited to settlement life.