Porous structure can effectively reduce the loads caused by the water wave, which results in lowering the cost of engineering project. The double porous shelter performs even better. Therefore, it receives much attention from researches. However, most of the previous studies dealing with the analysis of the interaction between water wave are porous structure were based on two-dimensional plane wave assumption. This can hardly reflect the real phenomena of complex wave action. In this paper, a semi-analytical solution to the hydrodynamic interaction between the three-dimensional short-crested wave and the cylindrical structure with double porous shelters is performed by employing the scaled boundary finite element method (SBFEM). The SBFEM possesses the advantages of finite element method (FEM) and boundary element method (BEM): the spatial dimension of the problem is reduced by one, no fundamental solution is needed and no singularity occurs. Meanwhile, this method can meet the infinity of the boundary condition automatically. In the SBFEM, the total computational domain is divided into three sub-domains, two ring-shaped finite sub-domains and one outer infinite sub-domain. A variational principle approach is proposed to establish the SBFE governing equations, which describe the variation of the velocity potential of wave motion in the radial direction. Bessel functions and Hankel functions are chosen as the basis functions for the solution of bounded and unbounded sub-domain problems, respectively. Numerical examples show that the proposed approach achieves very high accuracy and converges rapidly with quite few discretized nodes at the outer boundary. In comparison with the cylindrical structure with single porous shelter, the former performs better for the reduction of the water wave force. In addition, The influences of the wave parameters and the configuration of the structure on the system hydrodynamics, including the wave force, wave and diffracted wave contour are extensively examined. This research provides a valuable insight into the hydrodynamic analysis of cylindrical structure with double porous shelters and their structural design.