Two‐phase flow involving non‐Newtonian fluids in fractured media is of vital importance in many natural processes and subsurface engineering applications, such as rock grouting, groundwater remediation, and enhanced oil recovery. Yet, how the displacement dynamics is impacted by the non‐Newtonian rheology remains an open question. Here, we conduct primary drainage experiments in which a shear‐thinning Xanthan gum solution displaces a silicone oil in a transparent rough fracture for a wide range of shear‐thinning property (controlled by polymer concentration) and flow rates. We first evaluate the effects of shear‐thinning property on displacement efficiency. Based on qualitative and quantitative analyses of the observed fluid morphologies, we present an experimental phase diagram of the obtained displacement patterns. We characterize a novel displacement pattern where the fluid‐fluid interface changes from stable (plug flow) to unstable (fingering) as the fracture aperture, averaged over the transverse direction, varies along the mean flow direction. We demonstrate that the existence of this mixed displacement pattern can be explained by local viscosity heterogeneity induced by the coupling of the shear‐thinning behavior and the spatial variability of apertures. Finally, we propose a theoretical model elucidating the mechanisms behind the flow regime transitions. The interface stability criterion predicted by this model exhibits good agreement with the experimental measurements, and stresses the potentially important role of fluid rheology, coupled to aperture variability, in immiscible displacements in rough fractures. These findings provide new insights into the dynamics of immiscible two‐phase flows with non‐Newtonian effects, and has potential implications for the aforementioned engineering applications.This article is protected by copyright. All rights reserved.