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 alpha-helix structure above its phase separation temperature (T-p) but transforms into a solid-like aggregation composed of regular hexagonal packed cylinders below the T-p. 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 alpha-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 alpha-helix (T > T-p), (2) spherical aggregation composed of the hexagonal packed cylinder (T < T-p), 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 alpha-helix to the agglomeration containing hierarchical structures occurs in a stepwise manner when the temperature falls below the T-p, which might also be transition behavior similar to the process of protein folding through folding intermediates.