Dense and uniform initial packing structures of powders are of key significance in powder metallurgy process, which can provide the precondition for the fabrication of high-performance components with low cost and high efficiency. In this paper, the packing densification of indium tin oxide (ITO) granulated micro powders with continuous size distributions and internal porosity under three-dimensional vibrations was numerically investigated by discrete element method (DEM). Firstly, the DEM model was validated by physical experiments, and the contact parameters between particles and the porosity therein were determined. Then the effects of operating parameters on the macro/micro properties (e.g., packing density, coordination number (CN), pores, and forces) of the packing structures were analyzed. Results show that the mean CN cannot intuitively reflect the packing structure due to the complex and varied inter-particle contacts caused by the inhomogeneity of the particle size in a multi-sized granular system. Additionally, the excellent packing structure of porous ITO particles is always obtained from low amplitude when the vibration intensity is the same. Corresponding mechanism analyses reveal that higher amplitude normally causes strong convective diffusion, leading to more pores in the packing. This increases the probability of wedging effect occurring during settling, thereby reducing the packing density. However, optimal packing quality with low amplitude can only be achieved when coupled with high frequency. Therefore, applying vibration is an effective way to achieve dense packing of porous spherical particles, especially at low amplitude and high-frequency operating conditions.