Sargassum horneri has good economic traits and value, and its culture is gradually being emphasized. However, the suitable water depth for culture is still unclear, and the physiological characteristics and ecological functions of S. horneri in different water depths are also unclear. In this paper, we compared the primary productivity, nutrient uptake capacity, and algal trophic composition of S. horneri at different water depths (0.5 m and 2 m) based on light intensity in different water depths. The results showed that light intensity varied significantly (P < 0.05) with water depths and that the difference in light intensity due to water depth was significantly correlated with the primary productivity of S. horneri. The total productivity of S. horneri grown at 0.5 m water depth (upper layer) was significantly higher than that of S. horneri grown at 2 m water depth (lower layer) (P < 0.05), and S. horneri in the upper layer showed higher primary productivity and carbon sequestration capacity. The uptake of ${{\rm {NH}}_4^+} $ and ${{\rm {PO}}_4^{3-}} $ by the upper layer of S. horneri was significantly better than that of the lower layer of S. horneri under the light conditions (P<0.05), which has good potential in purifying the eutrophic water and regulating the ecological balance of the waters. However, the uptake of ${{\rm {NO}}_3^-} $ and ${{\rm {NO}}_2^-} $ by the upper layer of S. horneri is significantly lower than the lower layer of S. horneri (P>0.05), and it indicates that some strong light inhibition phenomenon occurs in S. horneri which affects the uptake of ${{\rm {NO}}_3^-} $ and ${{\rm {NO}}_2^-} $ by S. horneri. The moisture content of S. horneri at different water depths ranged from 71% to 75%, the ash content from 20% to 23%, the total lipids content from 6% to 8%, and the crude protein content from 8% to 10%. Nutrient composition did not differ significantly (P > 0.05) between the two water depth treatment groups. Studies have shown that by appropriately raising the culture layer, S. horneri can achieve higher productivity and nutrient uptake capacity, while the nutrient composition of S. horneri in the different water layers would remain relatively stable. This study has great significance for the technological development and upgrading of the artificial culture of S. horneri in natural sea areas as well as for the ecological environmental protection of sea areas.