An 8-week feeding trial was conducted to comprehensively investigate the effects of dietary phosphorus level and stocking density on tiger puffer. A 3 × 3 factorial design was used. The three dietary phosphorus levels were 0.68% (LP), 0.98% (MP), and 1.31% (HP) of dry matter, of which the available phosphorus level was 0.44%, 0.76%, and 1.06%, respectively. The three stocking density grades were 1.53 (LD), 2.30 (MD), and 3.06 (HD) kg m−3. The feeding trial was conducted in an indoor flow-through seawater system. Three replicate tanks were used for each group. The results showed that HP resulted in the highest growth rate. Higher dietary phosphorus levels reduced the whole-body lipid content, serum cholesterol contents, and hepatic mRNA expression of lipid metabolism-related genes such as ACACβ, DGAT1, and PPARα2. High stocking density levels reduced the growth rate and feed intake, but rarely affected other physiological parameters. Significant interactions were observed between effects of dietary phosphorus level and stocking density on phosphorus and calcium metabolism, but not between effects of both variables on the growth performance. Synergetic enhancement of phosphorus excretion by high phosphorus level and high stocking density was observed. These results shed new lights into the phosphorus physiology of marine fish and the interactions between phosphorus nutrition and rearing condition.