In order to understand the value of changes in fatty acid composition during early developmental stage of tawny puffer Takifugu flavidus, the fatty acid composition and content of tawny puffer in different developmental stages (unfertilized eggs, embryos 80–85 h after fertilization, newly hatched larvae 0-day-age, and before feeding larvae 3-day-age) were detected and analyzed by biochemical analysis methods. The results show that the moisture of egg and fry increased significantly with ontogenesis; the total lipid contents of fry decrease significantly with ontogenesis. 8 saturated fatty acids (SFA), 7 mono-unsaturated fatty acids (MUFA), and 12 poly-unsaturated fatty acids (PUFA) were found in the dry samples at different developmental stages. There was very similar tendency in fatty acid composition between unfertilized egg and its parent ovaries. At the embryonic period, the order of utilization rate of fatty acid was SFA (15.08%), MUFA (14.46%), n6PUFA (10.20%), and n3PUFA (0.19%), and C16:0, C16:1, C18:1n9c, and C18:2n6c were main sources of energy metabolism, and n3PUFA was preserved by priority, especially DHA, which was fully retained. After hatched, at the endogenous feeding stage, utilization rate of n3PUFA rose rapidly, followed by n3PUFA (19.60%), n6PUFA (16.98%), SFA (13.50%), and MUFA (13.01%). This was reverse to the embryo; C18:2n6c, C22:5n3(DPA), C20:5n3(EPA), C22:6n3(DHA), C18:1n9c, and C16:0 were main sources of energy metabolism, and the highest practical utilized quantity was DHA (14.44 mg/g), n3PUFA (especially DHA) was largely consumed before the larvae feeding. Therefore, larval development of tawny puffer needs to consume large amounts of n3PUFA (especially DHA and EPA). In larval breeding of tawny puffer, in order to improve the survival rate of larvae, enhancement of bait enriched with DHA and EPA (e.g., seawater rotifera, and Artemia sp. nauplii enriched with algae) was suggested.