The invention provides a method for screening beach shellfish larvae microalgae baits. The method is used for accurately screening beach shellfish larvae high-quality microalgae baits by quantitatively detecting composition of fatty acid and sterol in shellfish bodies after beach shellfish larvae intake mixed microalgae. The method provided by the invention is short in culture period, avoids probable influences of water-quality environmental conditions on the culture effect, and can be used for screening microalgae on the basis of the composition of fatty acid and sterol in the shellfish bodies. Therefore, the effect of the baits more fits in with selective ingestion and assimilation of the shellfish bodies during actual growth, so that the baits can be taken as high-quality baits for shellfish larvae.