The present invention discloses a mussel offspring seed cleaning apparatus, and aims to provide a mussel offspring seed cleaning apparatus with high working efficiency and low labor intensity, and capable of effectively cleaning up the impurities mixed in the mussel offspring seed. The apparatus includes a frame, a vibration residue filter device arranged on the frame, and a mussel scrubbing device arranged on the frame and located below the vibration residue filter device. The vibration apparatus residue filter device comprises an obliquely extending filter residue screen plate and an eccentric sheave mechanism disposed below the filter residue screen plate. The mussel rubbing device comprises a first vertical transmission belt and a second vertical transmission belt, which are symmetrically arranged; a first vertical scrubbing screen plate, a reversing plate and a second vertical scrubbing screen plate are sequentially arranged between the first vertical transmission belt and the second vertical transmission belt from top to bottom; a first scrubbing channel is formed between the first vertical scrubbing screen plate and the belt of the first vertical transmission belt; and a second scrubbing channel is formed between the second vertical scrubbing screen plate and the second vertical transmission belt.