A ball mill is used to separate the lignins of cotton stalk and these lignin are purified. Alkali lignin of KP and soda-AQ are separated and purified simultaneously. All of these lignins are analyzed by means of infrared spectroscopy. The results have indicated that the lignin in cotton stalk bark differs from the lignin in cotton stalk core; there are more parahydroxy phenylpropane and syringyl unit in cotton stalk bark and there are more guaiacyl unit in cotton stalk core; all of lignins have conjugated C=O and there is more conjugated C=O in cotton stalk bark than that in cotton stalk core. More parahydroxy phenylpropane in cotton stalk bark is delignified during cooking. This KP cooking is similar to soda-AQ cooking. More guaiacyl unit can be delignified during KP cooking than during soda-AQ cooking. There is alkyl hydrocarbon in sidepiece chain of all kinds of lignins.