Aggregates cause a fatal problem in the structural analysis of a biomacromolecule in solution using small-angle X-ray or neutron scattering (SAS): they deteriorate the scattering profile of the target molecule and lead to an incorrect structure. Recently, an integrated method of analytical ultracentrifugation (AUC) and SAS, abbreviated AUC–SAS, was developed as a new approach to overcome this problem. However, the original version of AUC–SAS does not offer a correct scattering profile of the target molecule when the weight fraction of aggregates is higher than ca 10%. In this study, the obstacle point in the original AUC–SAS approach is identified. The improved AUC–SAS method is then applicable to a solution with a relatively larger weight fraction of aggregates (≤20%).