The main feature that determines the self-assembly property and the structure of linear-hyperbranched copolymer consists of the architecture of the copolymer and exterior factors such as the solvent, initial copolymer concentration, crosslinking, and molecular recognition. To gain an understanding of the feature, hyperbranched polyphosphoramidate-poly(trimethylene carbonate) (HPPAE-PTMCn) copolymer with different topological structures was synthesized through chemical coupling reaction. HPPAE-PTMCn copolymer can form core-shell micelles. Via core-crosslinking, the stability of HPPAE-PTMCn micelles was enhanced and their comprehensive self-assembly behavior including its size, stability and morphology was further investigated by Transmission Electron Microscopy (TEM), dynamic light scattering and fluorescence analysis. Diameter of the core-crosslinked micelles increased with arm grafting ratio but decreased with arm length, which was contrary to their non-crosslinked analogues. Interestingly, a morphological transformation was observed after beta-CD was introduced to the copolymer solution as a result of host-guest inclusion complexation. TEM results revealed that HPPAE-PTMCn aggregates evolved from rods to a coexistence of rods and spherical micelles as the initial concentration increased and further to vesicles after increasing the molar ratio of beta-CD/PTMC segments.