The invention discloses a metagenome characteristic selecting method based on variable importance scoring and Neyman-Pearson detection. The method comprises the steps of 1, for one input metagenome classification operable unit dataset, calculating correlation between each microbe characteristic and a sample phenotype by means of symmetric uncertainty, screening the characteristics according to correlation scores, and generating a sub-dataset; 2, sampling the sub-dataset in a sampling-with-replacement mode, selecting first k characteristics by means of variable importance scoring, iterating thesteps, and after iteration, performing statistics on the number-of-appearances of each characteristic; and 3, calculating a threshold on the condition of a given parameter by means of a Neyman-Pearson detection method, performing screening and determining the characteristics with the number-of-appearances which is higher than the threshold as a candidate characteristic set, and determining the front k characteristics with highest number-of-appearances as a target characteristic subset. The metagenome characteristic selecting method has advantages of remarkably improving classification result,realizing higher stability and facilitating subsequent medical experiment of the metagenome by the generated candidate characteristic set.