Flat-panel detector (FPD) based dual-energy cone-beam computed tomography (DE-CBCT) is a promising imaging technique for dedicated clinical applications. In this paper, we proposed a fully analytical method for fast and effective single-scan DE-CBCT image reconstruction and decomposition. A rotatable Mo filter was inserted between an x-ray source and imaged object to alternately produce low and high-energy x-ray spectra. First, filtered-backprojection (FBP) method was applied on down-sampled projections to reconstruct low and high-energy images. Then, the two images were converted into a vectorized form represented with an amplitude and an argument image. Using amplitude image as a guide, a joint bilateral filter was applied to denoise the argument image. Then, high-quality dual-energy images were recovered from the amplitude image and the denoised argument image. Finally, the recovered dual-energy images were further used for low-noise material decomposition and electron density synthesis. Imaging was conducted on a Catphan® 600 phantom and an anthropomorphic head phantom. The proposed method was evaluated via comparison with the traditional two-scan method and a commonly used filtering method (HYPR-LR). On the Catphan® 600 phantom, the proposed method successfully reduced streaking artifacts and preserved spatial resolution and noise-power-spectrum (NPS) pattern. In the electron density image, the proposed method increased contrast-to-noise ratio (CNR) by more than 2.5 times and achieved <1.2% error for electron density values. On the anthropomorphic head phantom, the proposed method greatly improved the soft-tissue contrast and the fine detail differentiation ability. In the selected ROIs on different human tissues, the differences between the CT number obtained by the proposed method and that by the two-scan method were less than 4HU. In the material images, the proposed method suppressed noise by over 75.5% compared with two-scan results, and by over 40.4% compared with HYPR-LR results. Implementation of the whole algorithm took 44.5s for volumetric imaging, including projection preprocessing, FBP reconstruction, joint bilateral filtering, and material decomposition. Using down-sampled projections in single-scan DE-CBCT, the proposed method could effectively and efficiently produce high-quality DE-CBCT images and low-noise material decomposition images. This method demonstrated superior performance on spatial resolution enhancement, NPS preservation, noise reduction, and electron density accuracy, indicating better prospect in material differentiation and dose calculation.