Abstract: Flat-panel detector-based cone-beam computed tomography (CBCT) has demonstrated significant potential for applications in medical diagnostics and non-destructive testing. However, the coupling of stronger scatter artifacts and beam hardening effects in CBCT has long limited its quantitative imaging performance. Recently, a novel CBCT imaging technique called “spatial-temporal mixed spectral modulation” has been proposed. It can generate multi-energy spectral data with similar scattering distribution and good alignment of spectral projections, and it has the potential for multi-energy imaging with simultaneously scattering correction capability. This article presents an optimized design of the spectral modulator, which serves as the key hardware for the proposed imaging technique. We first determined the pattern of the spectral modulator based on its physics model and manufacturing difficulty. Subsequently, we selected the material, thickness, and period according to the analysis of the spectral imaging performance and the validation of scatter similarity hypothesis. Finally, we fabricated an overlapped spectral modulator with thicknesses of 0.2 mm + 0.4 mm Mo. Physical experiments demonstrated that this modulator can achieve enhanced CBCT quantitative imaging performance using the corresponding spectral-scatter decoupling algorithm.