In order to scientifically evaluate the soil fertility changes in the different densities of Jatropha curcas L. forest, the author did the soil microorganism research, with combination of water and fertilizer control technology measures, to improve the different densities of Jatropha curcas L. forest ecosystem environment, maintain its productivity level, to provide the basic data and the theoretical basis for scientific construction and management of Jatropha curcas L. forest, to accelerate its’ development. By comparing the soil microbial quantity and taxa to the three different densities of Jatropha curcas L. forests in Shuangbai, Yunnan Province. In addition, the author did the cluster analysis, and diversity index analysis to the Jatropha curcas L. forest of microorganisms. The results indicated that the three woodland of soil microorganism variance were remarkable, sample 2 was most, sample 1 and sample 3 had no differences. The vertical distribution showed that the microorganism quantity had difference, 0-15 cm soil bacteria, fungi number rose gradually, 11-15 cm peak; with the increase of soil depth, the number of fungi, bacteria showed a downward trend. Sample 2 species diversity index was also significantly higher than the other two kinds of forest lands, this might be due to moderate density was beneficial to the growth of the soil microorganism. Therefore, in the cultivation of Jatropha curcas L., the most suitable density of 2 m×3 m.