To demonstrate the clinical advantages of a deep-learning image reconstruction (DLIR) in low-dose dual-energy computed tomography enterography (DECTE) by comparing images with standard-dose adaptive iterative reconstruction-Veo (ASIR-V) images. In this Institutional review board approved prospective study, 86 participants who underwent DECTE were enrolled. The early-enteric phase scan was performed using standard-dose (noise index: 8) and images were reconstructed at 5mm and 1.25mm slice thickness with ASIR-V at a level of 40% (ASIR-V40%). The late-enteric phase scan used low-dose (noise index: 12) and images were reconstructed at 1.25mm slice thickness with ASIR-V40%, and DLIR at medium (DLIR-M) and high (DLIR-H). The 70keV monochromatic images were used for image comparison and analysis. For objective assessment, image noise, artifact index, SNR and CNR were measured. For subjective assessment, subjective noise, image contrast, bowel wall sharpness, mesenteric vessel clarity, and small structure visibility were scored by two radiologists blindly. Radiation dose was compared between the early- and late-enteric phases. Radiation dose was reduced by 50% in the late-enteric phase [(6.31 ± 1.67)mSv] compared with the early-enteric phase [(3.01 ± 1.09)mSv]. For the 1.25mm images, DLIR-M and DLIR-H significantly improved both objective and subjective image quality compared to those with ASIR-V40%. The low-dose 1.25mm DLIR-H images had similar image noise, SNR, CNR values as the standard-dose 5mm ASIR-V40% images, but significantly higher scores in image contrast [5(5-5), P < 0.05], bowel wall sharpness [5(5-5), P < 0.05], mesenteric vessel clarity [5(5-5), P < 0.05] and small structure visibility [5(5-5), P < 0.05]. DLIR significantly reduces image noise at the same slice thickness, but significantly improves spatial resolution and lesion conspicuity with thinner slice thickness in DECTE, compared to conventional ASIR-V40% 5mm images, all while providing 50% radiation dose reduction.