The Manila clam (Ruditapes philippinarum), with annual yield of 4 million tons in 2015, is a kind of important economic shellfish in China. The breeding technique in diked tidal flat which is the most productive technology, is not particularly reliable. In order to optimize it, a pond (A) was set up to induce phytoplanktonic blooms, which was regularly distributed to the nursery pond (B), and nursery pond (C) without algae superinduced as the control. The water, sediment quality and phytoplankton of A, B, C were compared with those of adjacent natural sea area (D). The growth of juveniles in B and C were also compared. The results showed that, there was no significant difference between A, B and C in water and sediment quality, but the water quality parameters(S, pH, DO, NH₃-N, NO₃-N, PO₄-P) and the sediment quality (organic carbon, sulfide) of the three ponds were significantly different from D; the phytoplankton density followed the order of A > B > C > D, but only A had significant difference with D; the shell length and density of juveniles in B were significantly higher than those in C. This indicated that there was a great difference in the environment between the diked tidal flat ponds and the natural sea area, and phytoplankton supplement can increase the growth and survival of the juveniles, thus ensuring the success rate of the breeding of R. philippinarum in diked tidal flat ponds.