The invention relates to an optimized configuration method based on mountain area layered rural water supply water source. The method comprises following steps: collecting data, identifying, establishing water demand units, revising the water demand units, calculating water demand, estimating water demand, secondary division and configuration, ordering water consumption and determining small type water supply devices. According to the method, water supply areas are divided on the basis of large water supply engineering, which can exert the water supply effect of the large water supply engineering to the most so that the large water supply engineering can be the water source for more water consumers and the drinking water security is guaranteed .During the division process, contour lines are used as factors for revision, which avoids unnecessary engineering investment and saves water supply cost. Secondary optimized configuration is performed on the mountain area water sources, which can reduce distributed water supply engineering distribution as much as possible and at the same time, the supplement effect of the distributed water supply engineering is exerted, which is convenient for management.