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Gelatin from the sea cucumber (Paracaudina chinens var.) was hydrolyzed by bromelain and the hydrolysate was found to have a high free radical scavenging activity. The hydrolysate was fractionated through an ultrafiltration membrane with 5 kDa molecular weight cutoff (MWCO). The portion (less than 5 kDa) was further separated by Sephadex G-25. The active peak was collected and assayed for free radical scavenging activity. The scavenging rates for superoxide anion radicals (O2·-) and hydroxyl radicals (·OH) of the fraction with the highest activity were 29.02% and 75.41%, respectively. A rabbit liver mitochondrial free radical damage model was adopted to study the free radical scavenging activity of the fraction. The results showed that the sea cucumber gelatin hydrolysate can prevent the damage of rabbit liver and mitochondria.