Polymer micelles with distinct morphologies and unique microphase separation microstructures can exhibit different properties and functions, holding great promise for a range of biomedical applications. In the current work, the topological effects of grafted triblock copolymers on the morphologies and microphase separation microstructures of micelles, including block arrangements and grafting arrangements of hydrophobic side chains, are systematically studied. Using common copolymer components of typical drug carriers, micelles with interesting geometries are achieved, such as raspberry, multicompartment, ellipsoidal and dumbbell shapes, in which the relationship between micelle morphology and copolymer topology is verified. With further exploration of the grafting position and amount of hydrophobic side chains, the microstructure influencing mechanism of copolymer micelles in self-assembly is discussed. The block arrangements of hydrophobic side chains determine the configurations of copolymers (zigzag/bridge) inside micelles, which in turn affect the morphological transitions (from spherical to ringed short-rods and then to cylinders) and the size of the hydrophobic ring, which further gradually change into hydrophobic cage. This study provides insight into the microstructure of hydrophobic side chain grafted copolymer micelles and further helps to understand the mechanism of controlling the morphology of micelles, which might be useful to guide the molecular design and experimental preparation of micelles with controllable morphology for drug encapsulation and delivery.