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Grazing is widely regarded as a critical factor affecting the vegetation community structure, productivity and nutritional value of natural grasslands. To protect and restore degraded grasslands, fencing is considered as a valuable tool. However, it is not clear whether long term fencing of grazers can improve the condition and nutritional values of vegetation community and soil properties. We have compared the impact of long term fencing and continuous grazing on vegetation community structure, nutritional values and soil properties of alpine meadow of the Qinghai-Tibet Plateau by field investigation (11-13 years) and indoor analysis during 2015-2017. Our results showed that long-term fencing clearly increased the above ground biomass and coverage of plant functional types. Long-term fencing improved the development of four plant functional types (GG, grass species group; SG, sedge species group; LG, leguminous species group and FG, forbs species group), but inhibited the growth of noxious species (NG). Long-term fencing significantly improved soil TN, TP, TK, AN, AP and AK in 0-10 cm soil layer, considerable effect on the improvement of soil TN, TP, AN, AP and AK in 10-20 cm soil layer and soil TP, AN, AP and AK in 20-30 cm soil layer were observed. However, long-term fencing significantly decreased biodiversity indicators i.e., Richness index, Shannon-Wiener diversity index and Evenness index of vegetation community. A substantial decrease in the density, biodiversity and nutritional values (CP, IVTD and NDF) of four edible plants functional types (GG, SG, LG and FG) were recorded. While a downward trend in the TN, AN, AP and AK of above ground biomass and soil were observed during 2015-2017 in alpine meadows due to long term grazing. The density, diversity and nutritional value (CP and IVTD) of long-term fencing alpine meadows showed a downward trend over time (2015-2017). By considering the biodiversity conservation and grassland livestock production, long-term fencing is not beneficial for the improvement of density, biodiversity and nutritional values of plant functional types. Thus, our study suggests that rotational fencing and grazing would be a good management strategy to restore and improve the biodiversity and nutritional values of plant functional types in natural grassland ecosystem.