Many challenges have been concentrated on the relationship between forest biodiversity and ecosystem functioning in ecology, since relative slower growth rate of tree and shrub species than herb species makes the tree biodiversity-ecosystem functioning interaction experiments become very difficult. In the past two decades, numerous experiments paid more attentions on the grassland and farmland ecosystem, and investigated the relationships between herbaceous plant species composition and ecosystem process. Theoretically, loss of the tree or shrub species might lead to the drastic changes in soil microbial community and enzyme activities in the fragile ecosystem, due to the sensitivity of soil microorganism to environmental change, which implies that we can understand the relationships between forest plant biodiversity and ecosystem process employing the method of simulated understory plant removal experiment. As yet, far less information has been available on the effects of forest plant loss on soil microbial community and enzyme activities. The subalpine forest located in the eastern Qinghai-Tibet Plateau and the upper reaches of Yangtze River is a typical high-frigid forest ecosystem and fragile ecosystem. Therefore, a three-year shrub and herbaceous plant removal experiment was conducted in the subalpine forest of western Sichuan, in order to understand the linkages of forest plant diversity with microorganism and enzyme activity in the forest soil, from July 2007 to July 2009. The understory removal experiments included the control (CK), herb layer removal (RH) and shrub layer removal (RS). Both shrub and herb plant removals changed soil microbial counts significantly. The ranked order of soil bacteria and fungi counts was CK > RH > RS, and the ranked order of actinomycete count was RH > CK > RS. Understory plant removal changed the composition of soil microbial community, and decreased the ratio of fungi in microbial community. The response of soil microbial community to shrub layer removal was more sensitive than that of herb layer removal. Meanwhile, the removal of shrub and herb layer decreased significantly the activities of invertase, urease, cellulose and dehydrogenase in soils, and the ranked order of incidence was CK > RH > RS. The effect of shrub layer removal on soil enzyme activity was more significant than that of herb layer removal. The results indicated that the removals of both shrub and herb layers altered the composition of soil microbial community and decreased the activities of the measured enzymes in soils of the studied plots, implying that the loss of plant species could change the soil microbial process in the high-frigid forest ecosystem. However, the present study only provides valuable information of short-term herb and shrub layer removal experiment, and long-term experiment needs to carry out in the future.