The characteristics of the sedimentary environment are considered significant for increasing the aquaculture production of Manila clams, Venerupis philippinarum. Among these, the grain size and sorting of the sediment, which determine the amount of pore-water-dissolved oxygen and organic matter content, can affect the growth and survival of clams. To determine the optimal grain size and sediment sorting in relation to the conditions of Manila clams (e.g., survival, growth, burrowing behavior, and condition index), we conducted three experiments. First, juvenile clams were incubated in four different grain sizes (coarse sand, 0.335–710 mm; medium sand, 0.180–0.335 mm; fine sand, 0.090–0.180 mm; and very fine sediment, < 0.09 mm). Survival was significantly higher in medium sand than in very fine sediment. The condition index of the Manila clams was higher in the medium sand than in the coarse and very fine sediments. However, the sediment grain size did not influence the shell growth or clam emergence behavior. Second, juvenile clams were incubated in three different treatments of sediment sorting (well-sorted sediment: 0.58 mm; moderately-sorted sediment: 0.46 mm; and poorly-sorted sediment: 0.37 mm). The shell growth rate was significantly higher in the poorly-sorted sediment than in any other treatment, while sediment sorting did not influence the survivorship, condition index, or emergence behavior. Third, juvenile Manila clams were incubated for 30 days in the sediment taken from two locations on the clam culturing mudflat, where a structure was installed to facilitate the settling of clam larvae (which was more poorly-sorted) or without a structure (the control). Although the survival and emergence behavior were not significantly different between the two treatments, the shell growth rate in the sediment under the structure was higher than that in the sediment with no structure. Moreover, the condition index of the Manila clams in the sediment under the structure was significantly higher than that under no structure. The results suggest that poorly-sorted sediment with an average grain size of medium sand is optimal for the survival and growth of Manila clams.