The invention discloses a reservoir tail reverse regulation method for native fish protection. The method comprises the steps that firstly, a breeding habitat of native fishes at the reservoir tail of a cascade hydroelectric dam is determined; secondly, the breeding characteristics of the migration native fishes are determined, and an ecological conservation project of a reach of the breeding habitat at the reservoir tail is carried out; then the length of the reservoir tail of a downstream hydropower station of a cascade hydroelectric project in March to May is determined by through a field investigation mode, and the maximum range of a natural river channel downstream of the upstream cascade power station is judged; and finally, the flow state of the reach at the reservoir tail is reversely regulated so as to achieve the goal of discharging water of the natural river channel at the reservoir tail and ensuring the natural flow state of the natural river channel.