Abstract Background. For medical imaging, usually, it is crucial to have high spatial resolution. Studies have demonstrated that the novel dual-layer flat panel detectors (FPDs) can acquire extra spatial information to enable super-resolution cone beam CT(CBCT) imaging compared to the conventional single-layer FPDs. Objective. The aim of this study is to investigate the feasibility of realizing near-isotropic super-resolution CBCT imaging with a dual-layer flat panel detector. Methods. To retrieve the near-isotropic super-resolution imaging information, a general mathematical signal model that includes the relative shift, namely, Δ u along the horizontal u -axis, Δ v along the vertical v -axis, between the two detector pixel arrays and the gap Δ d between the two detector layers, is established. Afterwards, an recurrent neural network-based deep neural network, named as two-dimensional 2D-suRi-Net, is employed to efficiently retrieve the projections having near-isotropic super-resolution imaging information. Numerical simulations were performed to investigate the impact of the relative shift (Δ u , Δ v ) and the gap Δ d under different scenarios. The real performance of this proposed super-resolution CBCT imaging approach is validated by a pig leg specimen and an intersecting cylinder phantom. Results. It is found that introducing half pixel shift, i.e. Δ u = Δ v = 0.5δdel ( δdel denotes the pixel dimension), between the two detector layers is necessary for super-resolution CBCT imaging, particularly when the detector gap Δ d is less than 3 mm. Results demonstrate that the proposed 2D-suRi-Net can effectively retrieve higher spatial resolution information from the acquired low-energy and high-energy projections having lower spatial resolution. Quantitatively, the spatial resolution difference between the reconstructed super-resolution CBCT images on the axial and coronal plane is less than 10%, demonstrating the near-isotropic super-resolution imaging capability of the 2D-suRi-Net method. Conclusion. In summary, this study demonstrates the feasibility of near-isotropic super-resolution CBCT imaging for dual-layer FPD based CBCT imaging systems.