Water stress is one of most common stress factors for vegetation. It can reduce cell water potential and stomatal conductance, thus may threaten the process of photosynthesis. Moreover, it can be noninvasively detected by using chlorophyll fluorescence, which is considered as the proxy of photosynthesis due to its sensitive to physiological change. However, chlorophyll fluorescence can be easily influenced by various factors, such as water stress, temperature, chlorophyll content, leaf and canopy structure. As a consequence, the relationship between chlorophyll fluorescence and water stress is significantly complicated. Thus, the study is focused on the rationale of chlorophyll fluorescence and its application in detecting water stress. Firstly, the origin of chlorophyll fluorescence in the view of photosynthesis was briefly introduced. Then, influence factors including chlorophyll content, leaf and canopy structure, ambient factors that affect chlorophyll fluorescence were analyzed. Furthermore, we summarized the application of chlorophyll fluorescence in detecting water stress. Finally, based on the above clarification, we proposed a new strategy of the application of chlorophyll fluorescence in water stress detecting.