Viscous fingering is a type of flow instability that occurs when a less viscous fluid displaces a more viscous fluid, causing instability at the displacement front. Owing to the opaque nature of porous media, experimental studies on the structure of viscous fingering and its development over time have been mostly limited to 2D porous media or Hele–Shaw cells. In this study, we used a micro-focused X-ray computed tomography scanner to investigate the 3D characteristics of viscous fingering in porous media. A low-viscosity iodine brine solution was injected in 3D-printed porous samples initially saturated by a high-viscosity syrup solution. The resulting miscible invasion was monitored by a sequence of X-ray tomography. Seven experiments were conducted to explore a large range of Péclet number and viscosity ratio. It allowed to identify the 3D morphology of fingering patterns and to quantitatively evaluate changes in physical properties such as iodine concentration in miscible fluids. As already identified in 2D experiments, characteristic events such as tip splitting, shielding, and coalescence were observed in 3D viscous fingering. At relatively low Péclet numbers, the fingering of the brine phase was more prone to breakthrough at certain points, forming a slender finger structure. As the Péclet number increased, the instability of the brine phase flow increased, making it easier to form multiple finger structures, and the tips were more prone to splitting into small finger structures. When the viscosity ratio decreased, the brine phase flow became more unstable. After halving the viscosity ratio of the miscible solution, multiple finger structures were formed at lower Péclet numbers, with small finger structures continuously splitting at the tips.