Stony corals (Scleractinia) harbor abundant toxins as part of their survival strategy, and these molecules also provide novel lead candidates for drug development. In this study, we present the first comprehensive investigation of toxin profiles of the understudied Goniopora columna through transcriptome analysis, which has expanded the biochemical diversity of marine organism derived toxins. Then, a novel Kunitz-like polypeptide, named GcKuz1, which exhibits therapeutic potential for thrombosis was selected for functional studies and mechanistic investigation. In vitro experiments revealed that GcKuz1, at 2-16 mu M, delayed plasma recalcification time and activated partial thromboplastin time without affecting prothrombin time. In murine models, GcKuz1, at 1-4 mg/kg dosage, significantly inhibited the FeCl3-induced carotid artery thrombosis and the carrageenan-induced mouse tail thrombosis. Moreover, GcKuz1 effectively attenuated thrombo-inflammation and cerebral tissue destruction, as well as restored blood-brain barrier integrity, in the transient middle cerebral artery occlusion model. Through enzyme kinetics assays and surface plasmon resonance (SPR) verification, GcKuz1 was shown to strongly inhibit the enzyme activity of plasma kallikrein (PKa) and FXIIa, two key factors involved in the contact-kinin pathway, via direct interaction, thereby exerting anticoagulation effects without impairing hemostasis. Notably, safety evaluation highlights the low toxicity, minimal hemolytic activity and reduced bleeding risk of GcKuz1, which underline its clinical availability. In conclusion, as a novel coral-derived protease inhibitor of FXIIa and PK, GcKuz1 offers potential therapeutic benefits in the treatment thrombosis-related cardiovascular diseases treatment by suppressing inflammation and preventing thrombus formation.