Fully atomistic molecular dynamic simulations were performed to address the self-assembly of amphiphilic and comb-like polybenzoxazines (iBnXz) in water, with i = 3 (trimer), i = 4 (tetramer); i = 6 (hemmer), i = 8 (octamer), and i = 10 (decamer). Spontaneous aggregation of these comb-like polybenzoxazine molecules into a single micelle occurs in the simulations. The simulations show that molecular size and concentration play important roles in micellar morphology. At an iBnXz concentration of 50 mM, the 3BnXz and 4BnXz molecules aggregate into spherical micelles, whereas the 6BnXz, 8BnXz, and 10BnXz molecules aggregate into cylindrical micelles. The micellar morphology is spherical at low concentrations, but undergoes a transition to cylindrical shape as concentration increases. The transition point depends on the molecular size-both the true size as indicated by molecular weight, as well as an additional effective size dependent on molecular flexibility.