The present study was conducted to investigate the effects of dietary phosphorus levels on the nutritional metabolism and intestinal microbiome of the GIFT tilapia (GIFT Oreochromis niloticus). Three isonitrogenous and isoenergetic diets with total phosphorus (P) content of 0.26% (low P treatment), 0.81% (moderate P treatment) and 1.51% (high P treatment) were prepared by using calcium dihydrogen phosphate as phosphorus source. Each diet was assigned to one treatment with four replicates and 30 fish per replicate. The fish with initial weight (8.42±0.09 g) were fed with the test diets for 8 weeks in an indoor recirculating aquaculture system (RAS). The results showed as follows: weight gain rate (WGR) and specific growth rate (SGR) of tilapia in moderate P treatment were significantly higher than those in low and high P treatments (P<0.05), and feed conversion ratio (FCR) of tilapia in moderate P treatment was the lowest. The hepatosomatic ratio, viscerosomatic ratio and condition factor showed a gradual decrease with the increase of dietary phosphorus level. Dietary phosphorus level had a significant effect (P<0.05) on the apparent digestibility of dry matter, crude protein, crude lipid and phosphorus in GIFT O. niloticus and they showed a trend of increasing and then decreasing with increasing dietary phosphorus level. KEGG annotation and enrichment analysis of differential metabolites showed that the main metabolic pathways of down-regulated differential metabolites were cyanuric acid metabolism, biosynthesis of gluconate ester, alanine, aspartic acid and glutamate metabolism, and most of the upregulated differential metabolites were mainly enriched in the metabolic pathway of fatty acid synthesis in the fish in low P treatment compared with those in moderate P treatment; most down-regulated differential metabolites were mainly enriched in the following metabolic pathways: arginine and proline metabolism, phenylpropionic acid biosynthesis and most up-regulated differential metabolites were mainly enriched in the metabolic pathways of amino sugars and nucleotide sugars in the fish in high P treatment compared with those in moderate P treatment. Ace, Chao1 and Shannon indices showed that the abundance and diversity of GIFT O. niloticus intestinal flora tended to increase with increasing levels of dietary phosphorus. Firmicutes, Actinobacteria, Proteobacteria and Bacteroidota were the dominant phyla in the intestinal flora of GIFT O. niloticus. The abundance of beneficial genera such as Romboutsia and Cetobacterium was the highest in the moderate P treatment while the abundance of Mycobacterium and Bacteroides showed a decreasing trend with increasing phosphorus content in the feed. In conclusion, moderate phosphorus in diet could improve the apparent digestibility of feed for GIFT O. niloticus, and phosphorus deficiency or excess in diet would inhibit amino acid metabolism. Phosphorus deficiency would accelerate the process of fatty acid synthesis. Appropriate phosphorus in diets could improve the abundance and diversity of bacterial flora, which may be beneficial to intestinal health.