The optimization of Na2SO3 concentration, pH value and protein precipitator YNB99-1 dosage in heparin sodium purification is studied with the even design method. The results indicate that when the concentration of Na2SO3 is 0.07 to approximately 0.08 mol/L, the dosage of protein precipitator is 0.5 g/L and the pH value is 3.0 to approximately 3.2, impurity protein can be deleted effectively and the active yield of heparin sodium can reach 99%.