The 4th order Darcy–Benard eigenvalue problem for the onset of thermal convection in a 3D rectangular porous box is investigated. We start from a recent 2D model Tyvand et al. (Transp Porous Med 128:633–651, 2019) for a rectangle with handpicked boundary conditions defying separation of variables so that the eigenfunctions are of non-normal mode type. In this paper, the previous 2D model (Tyvand et al. 2019) is extended to 3D by a Fourier component with wave number k in the horizontal y direction, due to insulating and impermeable sidewalls. As a result, the eigenvalue problem is 2D in the vertical xz-plane, with k as a parameter. The transition from a preferred 2D mode to 3D mode of convection onset is studied with a 2D non-normal mode eigenfunction. We study the 2D eigenfunctions for a unit width in the lateral y direction to compare the four lowest modes $$k_m = m \pi ~(m=0,1,2,3)$$, to see whether the 2D mode $$(m=0)$$ or a 3D mode $$(m\ge 1)$$ is preferred. Further, a continuous spectrum is allowed for the lateral wave number k, searching for the global minimum Rayleigh number at $$k=k_c$$ and the transition between 2D and 3D flow at $$k=k^*$$. Finally, these wave numbers $$k_c$$ and $$k^*$$ are studied as functions of the aspect ratio.
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