Large numbers of preferential flow paths exist in the multi-layer waterflooding reservoirs in high water cut stage.Being different with general oil reservoirs，the injection water obeys high velocity non-Darcy flow in the preferential flow paths. However，the present methods of development index prediction for the multi-layer waterflooding reservoirs do not take the preferential flow paths into account. Based on reservoir engineering theory and fluid mechanics in porous medium，considering the high velocity non-Darcy flow of injection water in the preferential flow paths，a method of development index calculation for multi-layer waterflooding reservoir was derived and proposed. This method can calculate the development indices such as water cut and oil recovery degree. It can reflect the effect of permeability and thickness of the preferential flow paths on production performance quantitatively. Results present that the interlayer contradiction increases with the increasing of permeability and thickness of the preferential flow paths. The recovery degree of normal reservoirs in the layer decreases. The injected water volume of the preferential flow path becomes larger，resulting in lower utilization factor of water injection and worse development effect. This method can exactly reflect the production characteristic of multi-layer waterflooding reservoir with preferential flow path and it can be used to guide the development adjustment for this kind of reservoir.