In this paper, the bandgap properties of three-dimensional holey phononic crystals with resonators are investigated by using the finite element method. The resonators are periodically arranged cubic lumps in the cubic holes connected to the matrix by narrow connectors. The influence of the geometry parameters of the resonators on the bandgap is discussed. In contrast to a system with cubic or spherical holes, which has no bandgaps, systems with resonators can exhibit complete bandgaps. The bandgaps are significantly dependent upon the geometry of the resonators. By the careful design of the shape and size of the resonator, a bandgap that is lower by an order of magnitude than the Bragg bandgap can be obtained. The vibration modes at the band edges of the lowest bandgaps are analyzed in order to understand the mechanism of the bandgap generation. It is found that the emergence of the bandgap is due to the local resonance of the resonators. Spring-mass models or spring-pendulum models are developed in order to evaluate the frequencies of the bandgap edges. The study in this paper is relevant to the optimal design of the bandgaps in light porous materials.