Thrombosis is a principle cause of cardiovascular disease, the leading cause of morbidity and mortality worldwide; however, the conventional anti-thrombotic approach often leads to bleeding complications despite extensive clinical management and monitoring. In view of the intense crosstalk between inflammation and coagulation, plus the contributing role of ROS to both inflammation and coagulation, it is highly desirable to develop safer anti-thrombotic agent with preserved anti-inflammatory and anti-oxidative stress activities. Nattokinase (NK) possesses many beneficial effects on cardiovascular system due to its strong thrombolytic and anticoagulant activities. Herein, we demonstrated that NK not only effectively prevented xylene-induced ear oedema in mice, but also remarkably protected against LPS-induced acute kidney injury in mice through restraining inflammation and oxidative stress, a central player in the initiation and progression of inflammation. Fascinatingly, in line with our in vivo data, NK elicited prominent anti-inflammatory activity in RAW264.7 macrophages via suppressing the LPS-induced TLR4 and NOX2 activation, thereby repressing the corresponding ROS production, MAPKs activation, and NF-κB translocation from the cytoplasm to the nucleus, where it mediates the expression of pro-inflammatory mediators, such as TNF-α, IL-6, NO, and PAI-1 in activated macrophage cells. In particular, consistent with the macrophage studies, NK markedly inhibited serum PAI-1 levels induced by LPS, thereby blocking the deposition of fibrin in the glomeruli of endotoxin-treated animals. In summary, we extended the anti-thrombus mechanism of NK by demonstrating the anti-inflammatory and anti-oxidative stress effects of NK in ameliorating LPS-activated macrophage signaling and protecting against LPS-stimulated AKI as well as glomeruler thrombus in mice, opening a comprehensive anti-thrombus strategy by breaking the vicious cycle between inflammation, oxidative stress and thrombosis.