To identify the dense packing of cylinder–sphere binary mixtures (spheres as filling objects), the densification process of such binary mixtures subjected to three-dimensional (3D) mechanical vibrations was experimentally studied. Various influential factors including vibration parameters (such as vibration time t, vibration amplitude A, frequency ω, vibration acceleration Γ) as well as particle size ratio r (small sphere vs. large cylinder), composition of the binary mixtures X_L (volume fraction of cylinders), and container size D (container diameter) on the packing density ρ were systematically investigated. The results show that the optimal vibration parameters for different binary cylinder–sphere mixtures are different. The smaller the size ratio, the less vibration acceleration is needed to form a stable dense packing. For each binary mixture, high packing density can be obtained when the volume fraction of large cylindrical particles is dominant. Meanwhile, increasing the container size can decrease the container wall effect and get higher packing density. The proposed analytical model has been proved to be valid in predicting the packing densification of current cylinder–sphere binary mixtures.