The invention provides a method and a system for determining protection width of an ecological filter strip. The method comprises the following steps: selecting a plurality of sample plots from the ecological filter strip, and selecting a plurality of sampling points in width direction of each sample plot; under an inflow condition, performing water sample collection from each sampling point, and detecting nutrient substance comprehensive removal rate of each sampling point; obtaining the distance between each sampling point and the upper edge of the ecological filter strip to obtain the width of the ecological filter strip of each sampling point, establishing a protective width model according to the width of the ecological filter strip of each sampling point and the nutrient substance comprehensive removal rate of the sampling point corresponding to the width; and determining the width of the ecological filter strip according to the protective width model. According to the method and the system for determining the protection width of the ecological filter strip, on the premise of ensuring that the ecological filter strip achieves the optimal purification function, the optimal protective width of the ecological filter strip can be reasonably and quantitatively determined, water purification is realized greatly, and the ecological benefit is effectively improved.