Packing densification of cubical particles under mechanical vibrations was dynamically simulated by using discrete element method (DEM). Effects of operating parameters such as vibration amplitude, frequency, vibration intensity, and container size (container wall) on packing densification were comprehensively investigated. The macro property such as packing density and micro properties such as coordination number (CN), radial distribution function (RDF), and particle orientation of the packings were analyzed and compared. It is found that mechanical vibration with proper vibration amplitude and frequency is effective for the densification of cubical particle packing. Packing structures of different packing densities display different properties, based on which random loose packing (RLP) and random close packing (RCP) of cubical particles are identified with the packing density of 0.591 and 0.683, respectively. Two densification mechanisms are discussed as the particle rearrangement is dominant for the transition from RLP to RCP and the crystallization along the container wall is dominant for the transition beyond RCP to ordering. The obtained results are useful for optimizing vibration conditions to generate dense packings and understanding the structural information of some fixed beds with cubical particles.