This study aimed to investigate the effects of different thermal treatments (steaming and baking) on the chemical compositions, total content of antioxidant components, and the antioxidant properties of soluble-free, soluble-conjugated, and insoluble-bound phenolics from tomato seeds. Total phenolic content (TPC) and free radical scavenging activities against ABTS•+, DPPH•, and peroxyl radicals were also investigated. As compared to the raw tomato seeds, phenolic compositions of tomato seeds in different phenolic fractions were significantly altered after thermal treatments. All thermal treatments did not significantly affect the TPC of the soluble-free phenolic fraction; however, they significantly increased the TPC values of the soluble-conjugated phenolic fraction. Steaming for 60 min significantly increased the radical scavenging activities against ABTS•+, DPPH•, and peroxyl radicals in the soluble-free and soluble-conjugated phenolic fractions. All thermal treatments had no prompt effects on the TPC values and free radical scavenging activities of the insoluble-bound phenolic fraction. Taken together, these results indicated that thermal treatments may alter the bioactivities of tomato seeds and steaming can be an effective way to obtain their health beneficial effects.