<p><i>Salmacis sphaeroides</i> and <i>Heliocidaris crassispina</i> constitute commercially valuable sea urchin species in the South China Sea. Large-scale production and wild population restoration of these species depend critically on hatchery-reared juveniles, necessitating the development of species-specific feeding protocols. This study systematically evaluated the efficacy of six natural macroalgae (<i>Ulva</i> sp., <i>Ulva lactuca</i>, <i>Gracilaria</i> sp., <i>Acanthophora spicifera</i>, <i>Spatoglossum</i> sp., and <i>Sargassum</i> sp.) versus a formulated feed on key aquaculture performance metrics, including survival rate (SR), specific growth rate of test diameter (SGR_D), specific growth rate of wet weight (SGR_W), and food conversion ratio (FCR). Comparative analysis showed divergent growth patterns between species: <i>S. sphaeroides</i> exhibited maximum SGR_D (3.47% d⁻¹) and SGR_W (9.82% d⁻¹) when fed <i>Sargassum</i> sp., whereas <i>H. crassispina</i> achieved peak growth performance with <i>Gracilaria</i> sp. (SGR_D: 2.87% d⁻¹; SGR_W: 9.42% d⁻¹). In contrast, both species demonstrated significantly suppressed growth under the formulated feed (<i>S. sphaeroides</i>: SGR_D 1.40% d⁻¹, SGR_W 4.77% d⁻¹; <i>H. crassispina</i>: SGR_D 1.73% d⁻¹, SGR_W 5.20% d⁻¹). Nutritional profiling identified <i>Gracilaria</i> sp. as the superior protein source (26.21% protein), associated with minimal FCR values (0.71 for <i>S. sphaeroides</i> and 0.52 for <i>H. crassispina</i>). Conversely, the formulated feed exhibited suboptimal characteristics, including prohibitive ash content (45.54%) and elevated FCR​. Notably, <i>U. lactuca</i> served as an optimal dietary component, sustaining superior growth performance and maintaining low nitrogenous waste levels (nitrite nitrogen: &lt; 1.63&#xa0;μmol L⁻¹; ammonium nitrogen: &lt; 16.50&#xa0;μmol L⁻¹) in the culture systems of both sea urchin species. The findings advance optimal feed formulation development for commercial aquaculture of these sea urchin species.</p>