The heterogenization of homogeneous metal complex catalysts has attracted great attention. The encapsulation of metal complexes into nanochannels of mesoporous materials is achieved by coating metal oxides at/near the pore entrance by diffusion-limited atomic layer deposition (ALD) to produce a hollow plug. The pore size of the hollow plug is precisely controlled on the sub-nanometer scale by the number of ALD cycles to fit various metal complexes with different molecular sizes. Typically, Co or Ti complexes are successfully encapsulated into the nanochannels of SBA-15, SBA-16, and MCM-41. The encapsulated Co and Ti catalysts show excellent catalytic activity and reusability in the hydrolytic kinetic resolution of epoxides and asymmetric cyanosilylation of carbonyl compounds, respectively. This ALD-assisted encapsulation method can be extended to the encapsulation of other homogeneous catalysts into different mesoporous materials for various heterogeneous reactions.