In order to optimize the extraction process of heparin sodium and analysis the structure. This article used central composite design and response surface to optimize the extraction process of heparin sodium’s enzymatic method. The heparin sodium with high purity was obtained after the resinous adsorption, precipitator for deproteinization, alcohol precipitation and column chromatography for further isolation and purification. Agarose gel electrophoresis, infrared spectroscopy (IR), ultra violet (UV) spectrum and nuclear magnetic resonance (NMR) used to identify the structure of heparin sodium elementarily. The optimum extraction conditions are extraction temperature 53 ℃, extraction time 4h and pH 8.5. The crude and purified product extraction yield are 0.81 % and 0.05 %, the rough and depurated goods potency are 6.5 U/mg and 108.3 U/mg by the method of ovine plasma, respectively. An IR spectrum shows the characteristic absorption peaks are 890 cm-1 and 940 cm-1, UV spectrum displays the maximum absorption wavelength is 205 nm. Combined with agarose gel electrophoresis and NMR, the rarefied product is identified as heparin sodium.