In recent years, the impacts of climate change have been the focus of world attention. As a result that water resource palys an important role in ecological, economic, and policy levels in Taiwan, the possible impact of extreme weather on river ecology is also a major research issue. Climate change may cause more climate variability and more frequent extreme hydrological events. In the past, lots of studies which related to climate change emphasis the impact of the average state of the river ecosystem, but less to the extreme weather in Taiwan. However, extreme events impacting on the ecological may be more deadly. Streamflow and water temperature play important roles in river ecosystem, which influences not only aquatic biodiversity but also the area of habitat. Especially for the Formosan Landlocked Salmon which is sensitive to habitat environment, they may be significantly influenced by greater variation of streamflow and higher water temperature due to climate change. As a result, it will be able to reflect the vulnerability of the habitat by evaluating extreme streamflow and water temperature under climate change. The habit of Formosan Landlocked Salmon, ChiChiaWan creek, is the main study area. A set of ecohydrological indicators is used to estimate the vulnerability of Formosan Landlocked Salmon’s habitat under climate change. The future climate scenarios are derived from several GCMs. Then, a hydrological model is used to simulate the extreme consecutive 7-day streamflow under different climatic conditions and a water temperature model is used to further simulate the extreme water temperature. In addition, this study combined water temperature data with the concept of vulnerability and reslilence that water temperature may exceed the threshold temperature of survival, and explored the impact on the habitat which caused by extreme streamflow and water temperature under the influence of extreme weather. According to the results of this study, streamflows will become much more extremalization with the increasing consecutive 7-day high flow and decreasing consecutive 7-day low flow under different climate scenarios. The results also show water temperature may exceed the threshold temperature of survival under some GCMs’ scenarios especially in winter. The frequency of high temperature event and maximum duration are increased, while the intensity of high-temperature events also trends to increase compared with the base period. No matter the frequency, duration, or strength of high temperature events, the results show that extreme weather may cause great impact and thus threaten the habitat of Formosan Landlocked Salmon.