Low-permeability oil and gas reservoirs have become one of the focuses of exploration and development worldwide, and waterflooding is a cost-effective method that has been utilized to enhance oil recovery in such reservoirs. Since the inevitable development of multiscale natural/artificial fractures and micronano matrix pores, the study for flow law of the fracture–matrix dual system becomes even more difficult. In this study, fractal characteristics of porous media and nonlinear flow behavior are taken into account to derive similarity criteria; then, 26 similarity criteria are proposed and carefully selected. To validate findings, three types of large-scale three-dimensional physical models with varying fracture scales were designed, based on the Yanchang Formation main reservoir in the Ordos Basin, and simulation experiments were carried out. The results indicate that the translation of experimental findings and oilfield applications can be effectively accomplished. Comparatively, driving pressure gradually increases during the water-free stage following a unique and noticeable “stepwise” fashion. As the number of fractures increases, the intensified imbibition effect leads to longer water-free oil production and a decrease in breakthrough pressure, particularly in sufficiently elongated rock samples. A two-phase flow threshold pressure gradient, which is greater than the minimum threshold pressure gradient, serves as a reliable indicator of reservoir production status and plays a crucial role in oilfield development. In addition, the waterflooding process of fractured cores can be divided into three stages: artificial fracture oil production, natural fracture oil production, and matrix area oil production. During these stages, the permeability decreases, the two-phase flow threshold pressure gradient increases, and water saturation at the isotonic point increases. Additionally, the number of fractures decreases, the range of the two-phase coflow zone decreases, and water relative permeability under residual oil saturation increases. This study provides a theoretical basis for effective waterflooding development and enhancement recovery of low-permeability reservoirs.