The freshwater eel Anguilla japonica is rapidly decreasing in number and has not yet been successfully mass produced. This may be at least partially attributable to the unique and long early life history of the eel. Therefore, we investigated its ontogeny of morphometry and growth pattern in larval stages to provide baseline information for understanding the early life history and improving seed rearing technology. This study was conducted for 200 days after hatching (DAH) and analyzed morphometry and allometry for eel larvae. The following cultured eel larval stages were identified: the yolk sac larvae stage (0–6 DAH, 3.23–6.85 mm total length (TL)), the pre-leptocephalus stage (7–30 DAH, 6.85–15.31 mm TL), and the leptocephalus stage (50–200 DAH, 15.31–60.06 mm TL). Cultured and wild eel larvae could be divided into characteristic larval stages at similar sizes. However, compared to wild eels, cultured eels had a slower growth rate and fewer preanal myomeres. Meanwhile, cultured eel larvae rarely had a mixed feeding period as the absorption of endogenous reserves was completed by 7 DAH. The lower jaw of eel larvae was significantly longer than the upper jaw from 50 DAH. In the pre-leptocephalus and leptocephalus stages, eel larvae showed continuous positive allometric growth at trunk height and tail muscle height with change to the willow leaf-like form. These growth characteristics may be the result of adaptation to the migration over long distances and to a diel vertical migration. The inflection point in the body parts growth patterns showed only before 30 DAH, and mass mortality appeared at this period. Therefore, to improve the growth and survival rates of cultured eel seed, it is necessary to focus on improving the feeding and rearing protocol until 30 DAH.