An integrated multi-trophic system consisting of white leg shrimp Litopenaeus vannamei and sea grape Caulerpa lentillifera was operated under various stocking densities and feeding rates to assess their effects on water quality, growth performance, and feed cost. The first experiment, which involved nursery rearing for 30 days, was designed in triplicate using a two-factor experimental design involving three stocking densities (1000, 2000, and 3000 ind. m−3) combined with two culture systems (monoculture and integrated system). Litopenaeus vannamei postlarvae 12 (PL12, mean weight: 3.33 ± 0.09 mg) and C. lentillifera (2 kg m−3) were applied in integrated tanks at a salinity of 30 g L−1. The results indicate that the integrated system of L. vannamei PL and C. lentillifera significantly decreased nitrogen and phosphorus levels and enhanced shrimp survival, growth rate, and yield. A significant synergistic effect between shrimp density and culture system was observed for shrimp survival (p < 0.05) and yield (p < 0.01). Higher shrimp density resulted in lower growth performance but increased yield. Applying stocking densities of 1000–2000 PL m−3 produced larger shrimp, while a density of 3000 PL m−3 obtained the highest production output in the integrated system. In the second experiment, the integrated system of juvenile L. vannamei (mean weight: 1.69 ± 0.07 g) and C. lentillifera was tested during the grow-out phase at different feeding rates. The six feeding treatments included a control group (monoculture) fed commercial feed (40% protein, 6% lipid) with a 100% feed ration (5% of biomass per day), while shrimp in the five integrated groups received commercial feed at 100, 75, 50, 25, and 0% feeding rations of the control. After 45 days of culture, the survival and yield of shrimp in the 100% and 75% feed ration treatments were significantly higher than those in the control group (p < 0.05). Nonetheless, shrimp growth steadily decreased with a reduction in the feeding rate from 50% downwards, and all groups grew significantly slower than the control group (p < 0.05). Interestingly, the feed conversion ratio and feed cost were lower at the lower feeding rates. This finding indicates that offering the L. vannamei—C. lentillifera integrated system at 75% feed ration can be considered the optimal feeding rate since it can reduce feed cost by 39.57% and improve water quality.