DEHCNPB (butyl-N,N-di(2-ethylhexyl)carbamoyl-nonylphosphonate) is an amido-phosphonic acid that has remarkable properties for the separation of uranium from wet phosphoric acid. Despite previous studies, a detailed description of the DEHCNPB organic solutions at the supramolecular and molecular scales is missing. In the present work, we use classical Molecular Dynamics (MD) combined with SANS and SAXS experimental data in order to describe the aggregation of the bifunctional extractant DEHCNPB as well as the speciation of uranium(VI) in such systems. We provide a fine description of the molecular species in the organic solution and of the interactions within the aggregates formed, shedding light on solvent extraction mechanisms. Without uranium, the organic phase is highly composed of dimers and trimers H-bonded through phosphonate functions and without water molecules. With uranium, two to three extractant molecules coordinate directly the uranyl cation by their phosphonate groups. Uranyl is not fully dehydrated in this organic solution, and the amide groups of the extractants are found to form H-bonds with the water molecules bound to uranyl. These H-bond networks around the metallic cation stabilize the complexes and facilitate the extraction. These results underline the importance of considering weak interactions in the understanding of extraction processes and demonstrate how molecular simulations provide essential insights into such complex organic phase chemistry with a high number of species.