This study focuses on the aggregation behavior of the biodegradable amphiphilic block copolymers based on methoxy poly(ethylene glycol) (mPEG) as a hydrophilic block and either crystalline poly(caprolactone-b-l-lactide) (P(CL-LLA)) or amorphous poly(caprolactone-b-D,L-lactide) (P(CL-DLLA)) as a hydrophobic block. These block copolymers have a strong tendency to form micelles in aqueous medium, with very low critical micelle concentrations (CMCs). The CMC of P(CL-LLA)-b-mPEG is higher than that of P(CL-DLLA)-b-mPEG when the mPEG block has the same molecular weight. Furthermore, the partition equilibrium coefficient (K(v)) of pyrene in the micellar solution of P(CL-LLA)-b-mPEG copolymer was lower than that of P(CL-DLLA)-b-mPEG copolymer when the mPEG block was the same length. These differences were believed to be related to the physical state of the core-forming blocks, i.e., the crystalline P(CL-LLA) block and the amorphous P(CL-DLLA) block. The TEM images showed that micelles formed by P(CL-LLA)-b-mPEG assembled in a cylindrical morphology, whereas those formed by P(CL-DLLA)-b-mPEG took a classical spherical shape. In addition, with differential scanning calorimetry (DSC) and wide-angle X-ray diffraction (WAXD) analyses, it is believed that the crystallization tendency of the core-forming blocks is the main factor governing the morphology of micelles in water. A possible mechanism for the cylindrical assembly morphology was discussed.