The Zoige Plateau is typical of alpine wetland ecosystems worldwide, which play a key role in regulating global climate and ecological balance. Due to the influence of global climate change and intense human activities, the stability and sustainability of the ecosystems associated with the alpine marsh wetlands are facing enormous threats. It is important to establish a precise risk assessment method to evaluate the risks to alpine wetlands ecosystems, and then to understand the influencing factors of ecological risk. However, the multi-index evaluation method of ecological risk in the Zoige region is overly focused on marsh wetlands, and the smallest units of assessment are relatively large. Although recently developed landscape ecological risk assessment (ERA) methods can address the above limitations, the final directionality of the evaluation results is not clear. In this work, we used the landscape ERA method based on land use and land cover changes (LUCC) to evaluate the ecological risks to an alpine wetland ecosystem from a spatial pixel scale (5 km × 5 km). Furthermore, the boosted regression tree (BRT) model was adopted to quantitatively analyze the impact factors of ecological risk. The results show the following: (1) From 1990 to 2016, the land use and land cover (LULC) types in the study area changed markedly. In particular, the deep marshes and aeolian sediments, and whereas construction land areas changed dramatically, the alpine grassland changed relatively slowly. (2) The ecological risk in the study area increased and was dominated by regions with higher and moderate risk levels. Meanwhile, these areas showed notable spatio-temporal changes, significant spatial correlation, and a high degree of spatial aggregation. (3) The topographic distribution, climate changes and human activities influenced the stability of the study area. Elevation (23.4%) was the most important factor for ecological risk, followed by temperature (16.2%). Precipitation and GDP were also seen to be adverse factors affecting ecological risk, at levels of 13.0% and 12.1%, respectively. The aim of this study was to provide more precise and specific support for defining conservation objectives, and ecological management in alpine wetland ecosystems.