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A novel method proposed by the author has been explicated, which means to analyze and study the atomic occupation problem of Li and Ni on 3a and 3b sites (belong to space group) in Li(Ni,Me)O2 (Me=Co, Mn or Co＋Mn) for Li-ion battery. This method is that with the help of the mixing occupation model of Li(Ni,Me)O2 and Power Cell 1.0 simulated computing program, the linear relationship between X-ray diffraction intensity ratio and the mixing occupation parameter x were obtained, and then using the data of the ratio of integrated diffraction intensity derived by the XRD experiment, the corresponding parameter x can be got from the simulated curves directly. Based on this method, the linear relationship between the square root of diffraction intensity ratio and the mixing occupation parameter x for 5 kinds of Li(Ni,Me)O2 materials were obtained. Applying this method to the study of the atomic occupation problem in the synthesis process of Li(Ni0.6Co0.2Mn0.2)O2, the relation of the mixing occupation parameter x and baking temperature has been found. Meanwhile, this method has been also used to investigate the transformation of the crystal structure and microstructure of Li(Ni1/3Co1/3Mn1/3)O2 in a 2H-graphite/Li (Ni1/3Co1/3Mn1/3)O2 lithium ion battery during charge-discharge process.