Commercial diets are widely used in aquaculture due to their cost-effectiveness and adequate nutritional for broad-diet species. However, carnivorous marine fish such as Asian seabass (Lates calcarifer), with limited capacity to digest plant-based feeds, require specialized feed additives to improve digestibility, promote growth, and support gastrointestinal health. This study aims to investigate the effects of feed additives (mannan oligosaccharides (MOS), Yucca Schidigera extract (YS), and solid-state fermented Aspergillus niger (SSF)), individually and in combination, on the growth, gut microbiota, and transcriptomic responses of juvenile L. calcarifer. A 70-day feeding trial was conducted with 10 dietary treatments, and growth performance and gut microbiota composition were assessed. Notably, fish fed with YS+SSF diet showed upregulation of growth-related genes, including ACTA1, CKMA, AMPD1, AK1, ATP2A1L, and CASQ1 and enrichment of KEGG and GO terms and pathways which are critical for muscle development, energy metabolism, cellular function, and calcium metabolism. Although gut microbiota diversity were reduced in fish fed with YS+SSF diet, this diet had enriched beneficial taxa such as Ralstonia and Lactobacillus which are crucial in nutrient digestion and feed utilization. These findings indicate that the synergistic effects of YS and SSF not only optimize gut microbial composition. but also activate host molecular pathways function to improve the growth of L. calcarifer.