A six-week feeding trial was carried out to investigate the impact of dietary ARA and CHOL levels, and their interactions, on the growth, lipid metabolism, and molting response of juvenile mud crabs (Scylla paramamosain) with an initial weight of 17.46 ± 0.04 g. A 3 × 3 two-factor design was adopted for 9 experimental diets with 0%, 0.75% and 1.5% ARA levels and 0%, 0.75% and 1.5% CHOL supplemental levels, respectively. The results showed that ARA and CHOL had significant interaction effects on percent weight gain and specific growth rate. Percent weight gain and specific growth rate of crabs fed 0.75% ARA diet were significantly higher than those of crabs fed 0% ARA diet, but only when dietary CHOL content was 0.75%. ARA and CHOL levels had significant interaction on crude lipid content and percentage of Oil Red O staining area in the hepatopancreas, and when 0.75% ARA was supplemented to 0.75% CHOL diet, the levels of crude lipid and percentage of Oil Red O staining area in hepatopancreas were significantly up-regulated. Moreover, 0.75% CHOL diet that was supplemented with 0.75% ARA significantly up-regulated the levels of DHA, EPA, and ARA in the hepatopancreas. Additionally, significant interactions between ARA and CHOL were found in expression levels of genes related to long-chain polyunsaturated fatty acid anabolism (Δ9 fad, elovl4, elovl5 and elovl6), fatty acid anabolism and catabolism (aco3, cpt1 and acc), fatty acid transport (fabp1, fabp3 and fatp4), and lipid catabolism and anabolism (hsl, srebp1, lpl and hl) in the hepatopancreas. 1.5% dietary ARA significantly increased the content of serum T-CHO and the activity of hepatopancreatic LCAT. The addition of 1.5% dietary CHOL significantly reduced the concentration of 20E in the serum. Furthermore, both 0.75% and 1.5% dietary ARA reduced concentrations of MIH and CHH in the serum. Significant interactions between dietary ARA and CHOL were observed in the concentrations of 20E and MIH in the serum. Dietary ARA significantly increased the expression levels of dib, e74b, e75 and ftz-f1 in the hepatopancreas. In conclusion, adding 6.02–11.06 mg/kg ARA to 1.21–1.27 mg/kg CHOL diets or adding 6.04 mg/kg ARA to 6.17–7.02 mg/kg CHOL diets both promoted cholesterol metabolism, deposition of essential fatty acids and lipids, and activated ecr-mediated molting response pathway, with these positive benefits likely resulting from a significant increase in PG.