The nonlinear flow regimes of a crossed fracture model consisting of two fractures have been investigated, in which the influences of hydraulic gradient, surface roughness, intersecting angle, and scale effect have been taken into account. However, in these attempts, the aperture of the two crossed fractures is the same and effects of aperture ratio have not been considered. This study aims to extend their works, characterizing nonlinear flow through a system of two intersecting fractures with different apertures. First, three experiment models with two fractures having different apertures were established and flow tests were carried out. Then, numerical simulations by solving the Navier-Stokes equations were performed and the results compared with the experiment results. Finally, the effects of fracture aperture on the critical pressure difference and the ratio of hydraulic aperture to mechanical aperture were systematically analyzed. The results show that the numerical simulation results agree well with those of the fluid flow tests, which indicates that the visualization techniques and the numerical simulation code are reliable. With the increment of flow rate, the pressure difference increases first linearly and then nonlinearly, which can be best fitted using Forchheimer’s law. The two coefficients in Forchheimer’s law decrease with the increasing number of outlets. When increasing fracture aperture from 3 mm to 5 mm, the critical pressure difference increases significantly. However, when continuously increasing fracture aperture from 5 mm to 7 mm, the critical pressure difference changes are negligibly small. The ratio of hydraulic aperture to mechanical aperture decreases more significantly for a fracture that has a larger aperture. Increasing fracture aperture from 5 mm to 7 mm, that has a negligibly small effect on the critical pressure difference will however significantly influence the ratio of hydraulic aperture to mechanical aperture.