The present invention discloses the expression method of natto kinase and its special expression vector and engineering bacterium. The expression vector is lactic acid bacteria constitutive expressionvector containing constitutive expression promoter, natto kinase leading peptide and its mature peptide coding sequence; or lactic acid bacteria inducing expression vector containing inducing expression promoter, transmembrane signaling peptide coding sequence, natto kinase leading peptide and its mature peptide coding sequence. Experiment shows that the expressed product of the engineering bacterium has relatively high fibrinolysis activity up to 41.7 urokinase unit each milliliter of the fermented supernatant, eating safety, no toxic side effect on human body and high stability, is suitablefor direct oral taking and may be added to various kinds of food. The present invention lays foundation for developing orally taken thrombolytic functional health food of natto kinase.