Asian seabass (Lates calcarifer ), a commercial marine species in Southeast Asia, is prized for its quick development and adaptability, but it is susceptible to various diseases, particularly in dense environments. This study investigated growth performance and gut microbiome diversity using 16S rRNA metagenomic analysis in juvenile Asian seabass supplemented with Mannan Oligosaccharides (MOS), Yucca Schidigera extract (YS), and Solid-State Fermented Aspergillus niger (SSF) to optimize aquaculture practices. Fish were fed commercial diets supplemented with ten additive compositions for 70 days, assessing growth performance, feed utilization, and survival. The YS_SSF group showed superior weight gain (WG = 36.05 ± 1.10) and specific growth rate (SGR = 1.36 ± 0.03), significantly outperforming the control group (WG = 24.79 ± 0.26, SGR = 1.07 ± 0.02, P < 0.05). Key genera linked to each diet were Burkholderiaceae and Weizmannia (YS_MOS), Enterobacterales and Pseudoalteromonas (SSF2), and Escherichia and Cytophagales (control). PICRUSt functional analysis revealed predominant pathways linked to amino acid and fatty acid biosynthesis as well as organic compound degradation. The Shannon index positively correlated with the Apparent Digestibility Coefficient (ADC) for phosphorus, protein, and lipids, as well as nutrient retention and growth rate. These results indicate MOS enhanced gut bacteria growth and nutrient digestibility; SSF enhanced feed efficiency from the breakdown of antinutrients; and YS promoted gut health and nutrient absorption. Combined feed additives, particularly SSF_MOS, showed great potential for promoting growth and feed efficiency in cultured fish.