The invention discloses a method and system for observing water temperature structural damage effect under reservoir flood impact. The method comprises following steps: time distribution regularity and space distribution regularity of the water temperature dynamic change under reservoir flood impact are observed, and the space distribution regularity of river way cross section observation vertical lines of water structural damage effect under reservoir flood impact is observed on the basis of the reality of a flood occurring process, a developing process and a dying away process when flood enters a reservoir, and in combination with river way longitudinal and cross section vertical water temperature dynamic change regularity in three water temperature distribution characteristic regions, wherein the water temperature distribution characteristic regions are a dam front water temperature layering region, a middle reservoir water temperature intermediate region, and a tail reservoir water temperature mixing region of a layering reservoir; the system comprises multiple observation sections and observation perpendicular lines uniformly distributed in the dam front water temperature layering region, the middle reservoir water temperature intermediate region, and the tail reservoir water temperature mixing region. The method and system are of great importance in increasing the technical level and achievement quality of water temperature change and distribution regularity systematic observation work of water bodies such as rivers and reservoirs, and are of great importance in pushing the industry technology development.