Pore structures of porous media and properties of fluid flow are key factors for the study of non-Darcy groundwater flow. However, it is difficult to directly observe pore structures and flow properties, resulting in a 'black box' problem of porous media. This problem has hindered the in-depth study of the groundwater flow mechanism at the pore scale. In recent years, 3D rapid prototyping technology has seen tremendous development. 3D printing provides digital models and printing models of porous media with clear internal structure. Thus, Lattice Boltzmann Method can be used to simulate the flow processes at the pore scale based on real pore structures. In this study, 3D printing cores and Lattice Boltzmann Method were coupled to conduct both laboratory and numerical experiments in spherical porous media with different sphere diameters and periodic arrays. The LBM simulation results show a good agreement with laboratory experimental results. With the advantages of LBM and 3D printing, this approach provides a visualization of the complex pore structure and fluid flow in pores, which is a promising method for studies of non-Darcy groundwater flow at the pore scale.