Ureido-modified poly(l-citrulline) (l-ornithine-co-l-citrulline denoted by PlOC) shows UCST-type phase separation behavior even under physiologically relevant conditions, which forms an α-helix structure above its phase separation temperature (Tp) but transforms into a solid-like aggregation composed of regular hexagonal packed cylinders below the Tp. This morphological transformation is characteristic of the phase separation behavior, but the mechanism behind it has remained incompletely understood. Here, we studied the phase separation behavior using small-angle X-ray scattering (SAXS) measurements. To analyze the SAXS data, we employed the modified unified model proposed previously, which decomposes the scattering profile into each structural element, such as the α-helices and their aggregation formed via hydrogen-bonding interactions between the ureido groups. The aggregation level is dependent on the temperature (T) and grouped into three classes: (1) mass-fractal aggregation composed of the α-helix (T > Tp), (2) spherical aggregation composed of the hexagonal packed cylinder (T < Tp), and (3) micro-order agglomeration formed by mutual fusion of the spherical aggregation, which appears as a solid-like aggregation. The SAXS analysis suggested that the transformation from the dispersed state as the α-helix to the agglomeration containing hierarchical structures occurs in a stepwise manner when the temperature falls below the Tp, which might also be transition behavior similar to the process of protein folding through folding intermediates.