In this report, we demonstrate the metal ion coordination-induced morphological transition of block copolymer assemblies under three-dimensional (3D) confinement. Polystyrene-block-poly(4-vinyl pyridine) (PS-b-P4VP) aggregates with various morphologies can be obtained by emulsion-solvent evaporation in the presence of metal ions (e.g., Pb(II) or Fe(III) ions) in the aqueous phase. Due to the coordination interaction between 4VP units and metal ions, the overall shape, internal structure, and surface composition of the particles can be tailored by varying the type and concentration of the metal ions. For example, when Pb(II) ions were employed, morphological transition of the assemblies occurred due to the formation of P4VP-Pb(II) complexes. More interestingly, when Fe(III) ions were added, hydrolysis of Fe(III) caused the reduction of the pH value of the aqueous phase, leading to the protonation of 4VP units. As a result, interfacial instability took place to trigger the splitting of emulsion droplets and then formation of nanosized micelles. Therefore, metal ion coordination is a facile strategy to tune the structure of assemblies under 3D confinement and offers an alternative approach for the design of organic-inorganic hybrid assemblies with well-tunable structures.