In this paper, a relative permeability prediction method considering the effects of capillary pressure and threshold pressure gradient in a low permeability fractal porous medium is established and analyzed based on the fractal approximation model that porous medium consist of a bundle of tortuous capillaries. With this method, every parameter has clear physical meaning without empirical constants, and the model's predictions have a good agreement with experimental data. In addition to this, it makes some discussions that how the characteristic parameters (such as tortuosity fractal dimension, pore fractal dimension, ratio of minimum-maximum capillaries diameters and threshold pressure gradient) influence the relative permeability. This study may be conducible to a better understanding of the mechanism for transient two-phase flow in the low permeability fractal porous medium.