The morphological evolution and phase transition of a branched crystalline-coil multi-block copolymer, poly(p-dioxanone)-block-poly(ethylene glycol) (PPDOstar-b-PEG), in aqueous solution under heating and cooling were investigated. The changes in size and morphology of the nano aggregates were monitored by dynamic light scattering (DLS), transmission electron microscopy (TEM) and atomic force microscopy (AFM). Semitransparent and uniform dispersion of nano aggregates with star anise-like morphology was obtained from PPDOstar-b-PEG at room temperature. The dispersion gradually turned transparent during heating to 80^oC because of the melting of the crystallized PPDO blocks. The crystals with low regularity melted first leading to a dissociation of the star anise nano aggregates to flake-like particles. The copolymer formed sphere-like micelles when temperature was high enough for melting all PPDO crystals. During the cooling run, hysteresis of phase transition was observed because of the supercooling of crystallization. The morphological evolution of the copolymer micelle suggested that the formation of the star anise-like nano aggregates was a hierarchical assembly process. A “crystallization induced hierarchical assembly” mechanism was therefore proposed to explain the formation of the star anise-like nano aggregates. Metastable flake-like nano particles formed at the initial stage of crystallization of PPDO blocks. The hydrophobic core of the flake was composed of several crystal lamellae or plates piled up layer by layer. With further crystallization of PPDO blocks, the flakes tended to aggregate because of the variation of hydrophilic-hydrophobic balance. The active edge of crystalline lamellae in the hydrophobic core of one flake may induce two different growth modes: epitaxial growth with amorphous spherical micelles and interparticle interpenetration crystallization in the amorphous region of other flakes. The branched structure of the nano particles was therefore formed driven by interparticle interpenetration crystallization and epitaxial crystallization simultaneously.