•The generation and development of eddy in fracture was observed using PIV.•The relationship between macroscopic nonlinearity and eddies was investigated.•The shrinking of effective aperture and losing of kinetic energy make flow nonlinear. The understanding of nonlinear flow in rough-walled rock fractures is critical for underground engineering and geological sciences. The macroscopic behavior and microfluidic field of flow in rough-walled artificial fracture models was investigated through microscopic visualization of hydraulic experiment. The results indicate that there are three states of flow regime in fracture, namely linear, weak inertial and strong inertial. In linear flow regime, the relationship between pressure drops and flow rate is linear, and all the streamlines in the microfluidic field are parallel. In weak inertial flow regime, pressure drop and flow become nonlinear, and the inertial pressure loss is less than the viscous pressure loss. Moreover, backflow occurs near the tortuous wall in the microfluidic field. In strong inertial flow regime, the inertial pressure loss is greater than viscous pressure loss, and the backflow begins to detach from the wall and eventually develop into a significantly large eddy far away from the wall. However, the flow in the mainstream remains laminar rather than turbulent in this experiment. This result indicates that the main cause of the nonlinearity of flow in fracture is eddies due to the increase of the inertia term and the variation of aperture. The shrinking of effective channel and losing of kinetic energy caused by eddies make fluid flow nonlinear. Moreover, the area and number of eddies depend on the fracture roughness and the Reynolds number.