Hyperuricemia is an important risk factor for many diseases including hypertension and type 2 diabetes. This study investigated and compared the effects of hydrolysates of two sea cucumber species, Apostichopus japonicus and Acaudina leucoprocta, on the alleviation of diet-induced hyperuricemia and renal inflammation. The structure and abundance of oligopeptides in enzymatic hydrolysates of A. japonicus (EH-JAP) and A. leucoprocta (EH-LEU) were identified via MALDI-TOF/TOF-MS, and the anti-hyperuricemic and anti-inflammatory effects of the hydrolysates were explored in a diet-induced hyperuricemic mouse model. Both EH-JAP and EH-LEU inhibit uric acid biosynthesis and promote uric acid excretion, leading to the alleviation of the hyperuricemic phenotype. In addition, these two treatments down-regulated the transcription of pro-inflammatory cytokines, up-regulated the transcription of anti-inflammatory cytokines, and inhibited the activation of the Toll-like receptor 4/myeloid differentiation factor 88/NF-kappaB (TLR4/MyD88/NF-κB) signaling pathway, leading to the alleviation of renal inflammation. EH-JAP had better effects than EH-LEU due to differences in their regulation of uric acid biosynthesis, uric acid excretion and release of anti-inflammatory cytokines. In addition, EH-JAP and EH-LEU treatment alleviated the dysfunction of the gut microbiota by increasing the abundance of beneficial Lactobacillus and short-chain fatty acid producers and decreasing the abundance of opportunistic pathogens. This study provides a valuable reference for the development of sea cucumber applications.