Alpine meadow is the major vegetation type in the Three River Headwater Region (THRD) and has been suffering degradation with different degrees due to overgrazing and global warming. Fencing is adopted worldwide to protect and restore the grassland ecosystem, but there still remains uncertainty about the efficiency and the proper duration of fencing. Although many studies have concluded that the degraded grassland has been improved after grazing exclusion from the perspective of increase in the total biomass, the community structure may sometimes become poor. However, most of the present studies were conducted using limited observation with a short duration and can't represent the overall picture of community structure changes objectively. Thus, the evaluation of community structure changes based on multi-site and long-term ground monitoring is required to indicate the effect of ecological restoration measures and to take reasonable measures in the THRD. In this paper, the aboveground biomass and biomass ratio of different economic groups at 57 sites were measured to indicate the community structure changes of alpine meadow after grazing exclusion from 2005 to 2017. The aboveground biomass was measured during the peak of growing season each year and plants were sorted into six plant economic groups including gramineae, cyperaceae, edible forb, inedible forb, poisonous grass, and leguminosae. There were two main comparative analysis of aboveground biomass, between the fenced and grazed sites and between years. The results showed that fencing enhanced the total aboveground biomass but not the productivity; the biomass of gramineae and cyperaceae in the fenced sites was significantly higher and edible forbs were significantly lower than those at the grazed sites, and others had no apparent difference; the community biomass had no significant change trend either at the fenced or grazed sites; the biomass proportion of gramineae and cyperaceae decreased by 48.2% and 23.9% respectively and poisonous grass increased by 230.2% during 2005—2017 at the fenced sites. At the grazed sites, the ratio of biomass of gramineae and cyperaceae decreased first and then increased, poisonous grasses and those of forbs were opposite, and all these were related with the implementation of balance measures between grass and livestock. It can be concluded that fencing not only has no significant influence on the total aboveground biomass but even aggravates the community structure of the alpine meadow in the Three-River Headwater Region. The results indicated that long-term grazing exacerbated community structure of alpine meadow and brought about both economic and ecological risks. Therefore, compared to grazing exclusion, which cut off the relationship between livestock and grassland, a more accurate balance measures between grass and livestock should be recommended.