Fish-aggregating devices play a significant role in tuna purse fisheries. The severe marine environment and the large number of non-biodegradable fish-aggregating devices impact structural safety and cause marine litter. Therefore, hydrodynamic performance and the use of biodegradable materials are crucial issues for ensuring the sustainability of fish-aggregating devices. In this study, a type of virtual biodegradable drifting fish-aggregating device (Bio-DFAD) was designed. Numerical simulations were conducted to investigate the motion responses and relative velocities of Bio-DFADs in regular waves (first- and fifth-order waves). The numerical model was applied based on unsteady Reynolds-averaged Navier–Stokes equations with the realizable k–ε model. For different scenarios of modeling, various conditions were modeled, including the relative length, wave steepness, and diameter of the balsa wood, to analyze their effects on the hydrodynamic response of the Bio-DFADs. The results indicated that the increased relative length, wave steepness, and diameter of balsa wood had a significant influence on the motion response amplitude operators (RAOs) and relative velocity of Bio-DFADs. The results suggested that a relative length (LF/B = 1.5) and smaller diameter (DF = 30 mm) were recommended for fewer motion responses and relative velocity. The obtained results provide insight for practical engineering applications of the hydrodynamic design of Bio-DFADs.