Well-defined block copolymers consisting of a hydrophilic poly (ethylene oxide) (PEO) and lipophobic poly (1H,1H-perfluorooctyl methacrylate) (PFOMA) were synthesized with controlled molecular weight via atom transfer radical polymerization (ATRP). The block copolymers formed stable micelles where PEO is the shell and PFOMA is the core in chloroform. The micellar morphology of PEO5K-b-PFOMA5K was found to be spherical with average diameter of ca. 12 nm, while meandering cylindrical with average diameter of ca. 13 nm was observed for PEO5K-b-PFOMA13K by TEM analysis. The self-assembled structures were reorganized to thermodynamically stable morphologies upon annealing above glass transition temperature (Tg). For example, spherical shape of PEO5K-b-PFOMA5K and cylindrical domain of PFOMA block in PEO5K-b-PFOMA5K became ordered cylindrical and continuous phase, respectively.