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Ecosystem functions are threatened by ongoing global biodiversity loss. Both Multifunctionality and realistic nonrandom extinction scenario are noteworthy approaches for valuing ecosystem function along with the biodiversity loss from the view of ecosystem management. We thus investigated four ecosystem functions simultaneously following potential species extinction scenarios seen in real Mongolian grassland. ANPP, forage nutrient values, litter decomposition and soil respiration were measured 1 and/or 2 years after the plant removal experiment. DNA sample of microorganisms extracted from the soil was subjected to the next-generation sequencing. Among ecosystem functions, ANPP and litter decomposition rate were decreased and forage quality was increased under random, rare species and dominants species first removal scenario, respectively. Diversity and species composition of soil microorganism was not patterned by plant species richness and removal scenario. Only the relationship between genus-level diversity of bacteria and ANPP had significant correlation among the microbial diversity and ecosystem functions. Because complimentarily effect worked against realistic species decline in Mongolian natural grassland, plant species loss not always lead to reduction of multiple ecosystem functions. However, each function responded differently to the species loss order, realistic nonrandom extinction scenario and multifunctionality approaches should be involved into the research between biodiversity and ecosystem functions to prepare for the ongoing biodiversity loss by various disturbances.