Structure and biodiversity of herbages were examined using the both transects and quadrats along topographical gradients on both shade and sunny slopes at the core zone of Three Rivers Sources Nature Protection Area. The relationships among richness index, diversity index and environmental factors (altitude, bare patch, slope, soil total carbon, soil total nitrogen, soil pH, soil total dissolved salt), disturbance intensity (rodent destroying and livestock grazing) were analyzed by factor analysis and partial correlation analysis. The results showed that the Margalef richness index of forbs had significant (P<0.01) correlation with the Margalef richness index of all species; the Margalef richness index for this two functional groups presented a peak with higher species diversity index in the communities of middle elevation on the sunny side; there was a positive correlation between the Margalef richness index of forbs and all species and altitude gradient on the shade slope. With the increase of altitude, there was not distinct change on Margalef richness index of grasses and sedges. According to the results of Factor Analysis (FA) and Partial Correlation, the First principal component, including soil patch, rodent disturbance and grazing intensity, significantly affected most of the biodiversity index of total species, except Margalef richness index of Cyperaceae, Simpson index of Gramineae and Pielou evenness index of Gramineae. So, the main factors influenced the diversity of all herbages on the sunny slope were soil patch, rodent disturbance and grazing intensity. Soil total carbon and nitrogen had significant effect on the diversity index and evenness index of grassed on the sunny slope. soil pH, total dissolves salt gathered with slope greatly influenced the richness index of sedges on the sunny slope. Altitude, soil total carbon and nitrogen, soil pH all had major effect on species diversity on the shade slope. The conclusions are that the spatial heterogeneity of species diversity resulted from the interaction of geographical environment (altitude, bare patch, slope), soil condition (soil total carbon, soil total nitrogen, soil pH, soil total dissolved salt) and disturbance intensity (rodent destroying and livestock grazing). At the small scale along the altitude gradient, the effect of the environment factor does not have significant effect on species diversity. Soil circumstance was the main Influencing factor for altering species diversity under no-disturbance or slight disturbance. Under heavy disturbance, intensity of disturbance had more significant influence on species richness and diversity than environmental factors. Reducing the heavy disturb such as grazing and rodent destroy was the first choice for preventing the degradation of alpine grassland and loss of herbage diversity in the alpine region.