The invention discloses a water resource configuration method facing river channel ecological water requirement. The method comprises the following steps: in a water resource configuration model, a river ecological water requirement section is defined as an ecological unit; a relation between a water resource and the ecological unit is built; the constraint of the water resource configuration model is met; a virtual reservoir is set near the upstream of the ecological unit to form the water resource configuration model facing ecological regulation; the water consumption of the ecological unitis 0; the capacity of the virtual reservoir is 0; and in the ecological regulation process, the water resource configuration model facing ecological regulation regulates according to the following rules: the discharge water quantity of the upstream reservoir and the section gathering currents both enter the virtual reservoir; the inflowing quantity is firstly used for supplying water to the ecological unit, and redundant water is discharged; and if the water supply of the ecological unit is insufficient, a water regulation instruction is sent to the upstream reservoir for ecological water supply. The method realizes multi-purpose long-series simulation process, meets the demands of different water use objects, and achieves important significance on development of comprehensive reclamationof river basins and on formulation of basin ecological water supply schemes on the planning aspect.