The invention discloses a schizothoracinae fish fertilized egg incubation method. The method includes the steps that firstly, a hatchery is selected, wherein A, the hatchery should be built on a river beach or mountain spring water downstream bottomland; B, water source construction is carried out, and a sandbank is arranged in the middle of a selected riverway; C, a pollution discharge ditch is distributed, a water channel lower than the hatchery is dredge in an underground area of the hatchery, river water is reserved on an upstream diversion dam and used for the pollution discharge ditch; secondly, the hatchery is built, wherein A, a hatching pond is built; B, a sunshade facility is erected; thirdly, the fertilized egg incubation method is carried out; fourthly, management is carried out. The fertilized egg incubation method includes the steps that firstly, the water amount of the hatching pond is controlled and water quality requirements are met; secondly, after fertilizer eggs basically absorb water, the fertilizer eggs are evenly distributed in the pond and do not accumulate; thirdly, fry which are just incubated are temporarily bred on the spot till the fry start to eat, and the fry are recycled after flat swimming. The method is easy and convenient to use, cost is low, operation is easy and convenient, the semi-natural hatchery is built in the position of a natural riverway, and the requirement of incubation work of hundreds of thousands to millions of schizothoracinae fish fertilized eggs is met.