The invention relates to the field of aquiculture, in particular to a mud flats shellfish intermediate cultivation pond and a cultivation method thereof. The invention provides the technical scheme that the mud flats shellfish intermediate cultivation pond comprises a pond and is characterized in that the middle of the pond is provided with the mud flats which are extended towards an opening of the pond, a plurality of troughs are respectively arranged among the mud flats as well as between the mud flats and the periphery of the pond, and the area of the mud flats is 50-70% of the total area of the pond; and the surfaces of the mud flats are respectively provided with a plurality of prevention nets, and the top of each prevention net is exposed out of the horizontal surface of the pond. By adopting the technical scheme, the invention provides the mud flats shellfish intermediate cultivation pond and the cultivation method thereof which are wide in application range, high in survival rate, high in income, and capable of being cultivated on a large scale.