Granular media constitute the most abundant form of solid matter on Earth and other astronomical objects. When external forces are applied to granular media, the forces are transmitted in the media through a network of contacts—force chains. Understanding the temporal evolution and spatial structure of these force chains constitutes a fundamental goal of granular mechanics. For decades, our understanding of force chains has been derived from 2D experiments, using quasi-2D photoelastic particles with various shapes. Here, we introduce a new experimental technique, which integrates photoporomechanics [1] into tomography, to observe the temporal evolution of 3D force chains under isotropic compression, triaxial shear and rotary shear. Our experimental study visualizes the alignment and intensification of 3D force chains as the external load changes from isotropic to triaxial shear and rotary shear. We also show that the fluctuation of the continuum-scale shear stresses can be pinpointed to the grain-scale buckling and healing of force chains. This work paves the way for understanding the grain-scale underpinning of localized failure of 3D granular media, such as shear banding of concrete structures and stick-slip frictional motion in tectonic and induced earthquakes.