Sinonovacula constricta is the first marine mollusc demonstrated to possess all fatty acyl desaturase (Fad) and elongase of very long chain fatty acids (Elovl) activities required for long-chain polyunsaturated fatty acids (LC-PUFA) biosynthesis via the Sprecher pathway, providing a good opportunity to investigate the essential fatty acids (FA) for its larval development. In the present study, we analyzed the Fad and Elovl expressions, FA compositions, and the feed effects of three representative microalgae (Chlorella sp., Chaetoceros calcitrans and Isochrysis galbana) in S. constricta at early developmental stages. The results showed that S. constricta Fad and Elovl were all highly expressed in zygotes, which might occur from maternal transfer. Compared to transcripts of Elovl4 activity, Elovl2/5 was only expressed relatively high in zygotes, indicating that C ≥ 22 LC-PUFA were more important than C ≤ 20 LC-PUFA for S. constricta larval development. The zygotes accumulated abundant FA from parents, especially eicosapentaenoic acid (EPA), but with small amount of docosahexaenoic acid (DHA). Meanwhile, the trochophore larva fed with single or mixed microalgae with I. galbana (rich in DHA) exhibited significantly higher growth and survival rate compared to those fed with single Chlorella sp. (rich in 18:2n-6 and 18:3n-3) and C. calcitrans (rich in EPA) or both of them. Those findings suggested that the highly expressed Fad and Elovl might be largely responsible for DHA biosynthesis, but this capability was limited to meet the developmental requirement and the dietary DHA was necessary. Taken together, our results compellingly demonstrated that DHA was essential for S. constricta larval development, which is important to guide its breeding.