To quantitatively describe the coupling between organism growth of several major organisms and nitrogen transformation in unfed sea cucumber-shrimp-macroalgae integrated multi-trophic aquaculture (IMTA) ponds, we established a pond nitrogen dynamics model based on the STELLA platform. The model coupled growth processes of phytoplankton, zooplankton, Ulva lactuca, Apostichopus japonicus, and Penaeus japonicus with the budget and transformation of particulate organic nitrogen (PON), dissolved organic nitrogen (DON), total ammonia nitrogen (TAN), nitrite nitrogen ( ${\mathrm{N}\mathrm{O}}_2^{-}\text{-}\mathrm{N}$), and nitrate nitrogen ( ${\mathrm{N}\mathrm{O}}_3^{-}\text{-}\mathrm{N}$) in water body and sediment. Model parameters were calibrated using data from one pond and independently validated with another pond without changing the parameter values. The absolute values of average relative errors for organism biomass and major nitrogen forms were ≤0.18 in the calibration pond and ≤0.15 in the validation pond. The agreement for sediment nitrogen was better than that for water nitrogen. Flux analysis showed that TAN in water body was primarily supplied by ammonification and removed through phytoplankton uptake and ammonia volatilization. PON in sediment was primarily derived from fecal input of cultured animals and transformed through sea cucumber feeding and microbial degradation. TAN in sediment was further removed through ammonia oxidation, denitrification, and anaerobic ammonium oxidation. The model represents the dynamic coupling between organism growth and water body-sediment nitrogen cycling in unfed sea cucumber-shrimp-macroalgae IMTA ponds and maintains stable simulation performance in cross-pond validation.