Two-phase flow interfacial dynamics in rough fractures is fundamental to understanding fluid transport in fractured media. The Haines jump of non-Darcy flow in porous media has been investigated at pore scales, but its fundamental processes in rough fractures remain unclear. In this study, the micron-scale Haines jump of the air-water interface in rough fractures was investigated under drainage conditions, with the air-water interface tracked using dyed water and an imaging system. The results indicate that the interfacial velocities represent significant Haines jumps when the meniscus passes from a narrow "throat" to a wide "body", with jump velocities as high as five times the bulk drainage velocity. Locally, each velocity jump corresponds to a fracture aperture variation; statistically, the velocity variations follow an exponential function of the aperture variations at a length scale of ~100 µm to ~100 mm. This spatial-scale-invariant correlation may indicate that the high-speed local velocities during the Haines jump would not average out spatially for a bulk system. The results may help in understanding the origin of interface instabilities and the resulting non-uniform phase distribution, as well as the micron-scale essence of the spatial and temporal instability of two-phase flow in fractured media at the macroscopic scale.