In order to analyze the lipid compositions and antioxidant activities of Hemicentrous pulcherrimus and Strongylocentrotus nudus gonads, the lipid and fatty acid compositions were analyzed by NMR and GC-MS, and the antioxidant activities were determined by the methods of DPPH radical scavenging, hydroxyl radical scavenging and superoxide anion radical scavenging in this paper. The experimental results indicated that the triacylglycerols and phospholipids were the predominant lipid components of H. pulcherrimus and S. nudus gonads, while the contents of free fatty acids, cholesterol and cholesteryl esters were relatively low. Meanwhile, C20:4n-6 and C20:5n-3 were the major polyunsaturated fatty acids, and the total contents of C20:4n-6 and C20:5n-3 reached respectively 35.88% in H. pulcherrimus and 34.98% in S. nudus. The remarkable differences were observed in the fatty acid compositions of neutral lipids and polar lipids. Neutral lipids were chiefly composed with C14:0 and C16:0, whereas polar lipids mainly of C20:4n-6 and C20:5n-3. H. pulcherrimus and S. nudus gonad lipids exhibited great scavenging activity on DPPH radical and hydroxyl radical. The IC₅₀ values of H. pulcherrimus and S. nudus gonad lipids to DPPH radical were 2.75 and 1.98 mg/mL, and were 0.33 and 0.29 mg/mL to hydroxyl radical, 0.33 and 0.31 mg/mL to superoxide anion radical, respectively. The results suggested that H. pulcherrimus and S. nudus gonad lipids had high nutritional values and antioxidant activities, and could be the important dietary sources of C20:4n-6, C20:5n-3 and phospholipids.