The three-dimensional (3D) confinement effect on the microphase-separated structure of a diblock copolymer was investigated both experimentally and computationally. Block copolymer nanoparticles were prepared by adding a poor solvent into a block copolymer solution and subsequently evaporating the good solvent. The 3D structures of the nanoparticles were quantitatively determined with transmission electron microtomography (TEMT). TEMT observations revealed that various complex structures, including tennis-ball, mushroom-like, and multipod structures, were formed in the 3D confinement. Detailed structural analysis, showed that one block of the diblock copolymer slightly prefers to segregate into the particle surface compared with the other block. The observed structures were further elaborated using cell dynamics computer simulation. (C) 2016 Wiley Periodicals, Inc.