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Fuzzy clustering analysis is a widely used fuzzy mathematics method ,which could be applied in various fields. Based on the fuzzy set theory, application of fuzzy clustering analysis in microbial enhanced oil recovery (MEOR) was studied. At first, strains which had ability to produce biosurfactant were selected as part of the statistical indicators. Then data were corrected and standardized by empirical formula. Similarity matrix was established with angle cosine. After that, clustering analysis was made and evaluated by Transitive Closure. Finally, the strain which had the best adaptability to the oilfield conditions was chosen by fuzzy cluster analysis. And so the optimal choice mechanism was established.