In this paper we propose and analyze an energy stable numerical scheme for the square phase field crystal (SPFC) equation, a gradient flow modeling crystal dynamics at the atomic scale in space but on diffusive scales in time. In particular, a modification of the free energy potential to the standard phase field crystal model leads to a composition of the 4-Laplacian and the regular Laplacian operators. To overcome the difficulties associated with this highly nonlinear operator, we design numerical algorithms based on the structures of the individual energy terms. A Fourier pseudo-spectral approximation is taken in space, in such a way that the energy structure is respected, and summation-by-parts formulae enable us to study the discrete energy stability for such a high-order spatial discretization. In the temporal approximation, a second order BDF stencil is applied, combined with an appropriate extrapolation for the concave diffusion term(s). A second order artificial Douglas-Dupont-type regularization term is added to ensure energy stability, and a careful analysis leads to the artificial linear diffusion coming at an order lower than that of surface diffusion term. Such a choice leads to reduced numerical dissipation. At a theoretical level, the unique solvability, energy stability are established, and an optimal rate convergence analysis is derived in the $ℓ$^∞(0,$T$;$ℓ$²)∩$ℓ$²(0,$T$;$H_N^3$) norm. In the numerical implementation, the preconditioned steepest descent (PSD) iteration is applied to solve for the composition of the highly nonlinear 4-Laplacian term and the standard Laplacian term, and a geometric convergence is assured for such an iteration. Finally, a few numerical experiments are presented, which confirm the robustness and accuracy of the proposed scheme.