The Manila Clam is an important economic shellfish in China’s seafood industry. In order to improve the design of juvenile Manila Clam seeding equipment, a juvenile clam discrete element method (DEM) particle shape was established, which is based on 3D scanning and EDEM software. The DEM contact parameters of clam-stainless steel, and clam-acrylic were calibrated by combining direct measurements and test simulations (slope sliding and dropping). Then, clam DEM simulation and realistic seeding tests were carried out on a seeding wheel at different rotational speeds. The accuracy of the calibrated clam DEM model was evaluated in a clam seeding verification test by comparing the average error of the variation coefficient between the realistic and simulated seeding tests. The results showed that: (a) the static friction coefficients of clam-acrylic and clam-stainless steel were 0.31 and 0.23, respectively; (b) the restitution coefficients of clam-clam, clam-acrylic, and clam-stainless steel were 0.32, 0.48, and 0.32, respectively. Furthermore, the results of the static repose angle from response surface tests showed that when the contact wall was acrylic, the coefficient rolling friction and static friction of clam-clam were 0.17 and 1.12, respectively, and the coefficient rolling friction of clam-acrylic was 0.20. When the contact wall was formed of stainless steel, the coefficient rolling friction and static friction of clam-clam were 0.33 and 1.25, respectively, and the coefficient rolling friction of clam-stainless steel was 0.20. The results of the verification test showed that the average error between the realistic and simulated value was <5.00%. Following up from these results, the clam DEM model was applied in a clam seeding simulation.