Napahai wetland is a unique and seasonal marsh wetland located in the middle of Hengduan Mountains, northwestern Yunnan Plateau. In the recent decades, it has been seriously degraded under human disturbances, mainly including drainage and overgrazing. In the present paper, two kinds of typical degradation transects were established to evaluate the synergistic impacts of overgrazing stress and water regime and the single impacts of overgrazing stress in the lakeside of Napahai. The two transects were further classified into four degradation gradients, including primary wetland(PW), lightly degraded wetland (LW), moderately degraded wetland (MW) and severely degraded wetland (SW). Cluster analysis and principal component analysis (PCA) were conducted to explore the process and mechanism of wetland degradation as well as to evaluate the degree of wetland degradation quantitatively at system level of "vegetation-water-soil". The results were as follows: the numbers of plant families, genera and species as well as species diversity and richness all increased gradually from PW to SW, whereas species evenness remained stable. The plant community succession is in the direction of aquatic plant community→swamp plant community→swamp meadow plant community →meadow plant community. Correspondingly, the community changed towards more complicated structure characterized by the decreasing of helophyte and increasing of hygrophyte and mesophyte. Overgrazing stress changed the inherent mode of plant community succession and accelerated the degraded stage of "swamp meadow community" to some extent, although the direction of succession had not changed. The degradation characteristics of water properties varied in different disturbance type, the water indices of salinity, total alkalinity, total hardness, total nitrogen, ammonia nitrogen, nitrate nitrogen and total phosphorus all increased along the GD gradients, whereas decreased along the GAD gradients, depending on the water regime. Therefore, hydrologic alteration had a significant effect on wetland water properties. The changes of wetland soil properties were similar in the two disturbances. Among them, the contents of organic matter, total nitrogen and available nitrogen decreased, total phosphorous and total potassium (K) increased, whereas the available phosphorous and available potassium (K) showed no obvious changes. The vertical distribution for each nutrient content in the soil profiles of degraded wetlands varied greatly. Soil total phosphorous, available phosphorous and available potassium (K) decreased along the soil depth gradients. It showed that soil nitrogen content was the most obvious characteristics of wetlands degradation. In order to identify the driven factors of wetlands degradation under the multi-factorial stresses, PCA was employed to synthesize the degradation information from multiple aspects as discussed in this paper. Thirty indices based on vegetation, water and soil were simplified into three principal components by PCA, explained 54.8%, 29.1% and 15.9% of the total variance, respectively. PCA results indicated that plant community was the most representative of wetlands degradation, and the soil structures and nutrient contents changed significantly along the degradation gradients of lakeside wetlands, Napahai. By contrast, the contributions made by water nutritional contents were lowest compared with vegetation and soil for wetlands degradation. Based on the three principle components derived from PCA, a multiple linear regression model, PC=0.548×PC1+0.291×PC2+0.159×PC3, was conducted to calculate the scores for each degradation stage, which could be taken to evaluate the wetlands degradation.