Lipid class and fatty acid (FA) analysis were conducted on newly molted, fed, and starved zoea V and megalopa of the mud crab, Scylla serrata (S. serrata). Larvae starved for 4 d showed a substantial decrease in total FA content, from 49.67 μg/mg to 13.94 μg/mg ash‐free dry weight (AFDW) at the zoea V stage, and from 38.47 μg/mg to 10.40 μg/mg AFDW at the megalopa stage. This depletion indicates that S. serrata larvae effectively utilize stored lipid reserves for energy during periods of food deprivation. Megalopa subjected to longer starvation periods, however, did not utilize lipid as the major energy source after day 4, suggesting increased reliance on protein catabolism during prolonged starvation. At both larvae stages the major FAs were 18:1n‐9, 16:0, 20:5n‐3 (eicosapentaenoic acids, EPA), 18:3n‐3 (linolenic acid, LNA), 18:0 and 22:6n‐3 (docosahexaenoic acid, DHA) and this FA profile persisted in both fed and starved larvae. The highly unsaturated fatty acids (HUFA), EPA, DHA, and arachidonic acid (20:4n‐6, AA) were not conserved in tissue during starvation, indicating that HUFA requirements might be lower for S. serrata larvae than shown for other crustaceans. Similarly, a high level of LNA in newly molted zoea V and megalopa were rapidly depleted in unfed larvae, indicating that this FA had an important role as an energy reserve. Throughout the study, FAs from the polar lipid fraction dominated larvae tissues, while FAs from the neutral lipid constituted the largest accessible energy reserve during starvation (depleted from 23.05 to 1.23 μg/mg AFDW in zoea V, and from 19.00 to 1.27 μg/mg AFDW in megalopa). The results of this study provide new insight into lipid utilization of S. serrata larvae during development, an important step toward development of formulated diets for use in mud crab hatcheries.