The lined seahorse (Hippocampus erectus) is a rare and valuable aquatic species with significant utilitarian value. Enhancing the growth and survival rates of juvenile lined seahorses is essential to address their high mortality rates, thereby aiding in resource recovery and artificial cultivation. This study conducted a 45-day feeding experiment using brine shrimp (Artemia salina) enriched with Astragalus polysaccharide (APS), Lentinus edodes polysaccharide (LNT), and Lycium barbarum polysaccharide (LBP) to feed juvenile lined seahorses. We assessed the effects of these three naturally extracted polysaccharides on growth performance, survival rate, intestinal morphology, physiological enzyme activities, and intestinal microbiota. The results showed that supplementation with these polysaccharides significantly enhanced the growth performance and survival rates of juvenile seahorses compared to the control group without polysaccharide enrichment (P < 0.05). Survival rates increased from 36 % in the control group to over 55 % with polysaccharide supplementation. Histologically, all three natural polysaccharides significantly improved the intestinal morphology of the juveniles, including increases in mucosal height, width, and muscle thickness. Physiologically, these polysaccharides positively influenced the activities of digestive, immune, and antioxidant enzymes. Analysis of the intestinal microbiota revealed that polysaccharide supplementation significantly increased the total bacterial count and community diversity, promoting the growth of beneficial bacteria while inhibiting harmful ones at both the phylum and genus levels. Functional prediction of the intestinal microbiome indicated that microbial genes were predominantly enriched in metabolic pathways, confirming the potential benefits of these polysaccharides in promoting intestinal health. Overall, our findings suggest that supplementation with APS, LNT, and LBP effectively enhances the growth performance and survival rates of juvenile seahorses by improving their physiological conditions, intestinal structure, and microbiota. This study underscores the significance of naturally extracted polysaccharides in the cultivation of juvenile lined seahorses, offering new avenues for promoting healthy aquaculture practices and providing empirical support for their use as supplements in aquatic organisms.