In this study, a novel HKUST-1-based nanocomposite was fabricated through a facile in-situ solvothermal method using amino-tethered SBA-15 (APTMS-SBA-15) as the matrix. Several characterizations had been applied to study the physicochemical properties of the hybrid material. The APTMS-SBA-15, acting as a structure-directing agent, could not only induce the nucleation of HKUST-1 directionally through the coordination effect between Cu2+ centers and amino groups, but also regulate the growth of the nanocrystals via the confinement effect of mesoporous structure. The HKUST-1 grains transformed from octahedron (10–15 μm) to hierarchical flower-like architecture assembled by lamellar crystals (100–200 nm in thickness). The smaller crystal sizes along with the extra ordered mesopores were conducive to reducing the intragranular mass transfer resistance and shortening the diffusion path of CO2 transport. Compared with pristine HKUST-1, the specific surface area, micropore volume and the amount of exposed metal sites increased simultaneously. Meanwhile, the retained amino could also contribute to polarized surfaces of the framework, thus enhancing the interaction towards CO2 molecules. The adsorption sites originating from HKUST-1 synergized with APTMS-SBA-15 to promote the effective capture of CO2. At 25 °C and 1.0 bar, the CO2 adsorption capacity and CO2/N2 (15%/85%) selectivity of the composite reached 4.93 mmol/g and 18.3, which were increased by 18.5% and 92.6% respectively than those of pure HKUST-1. These findings provided a promising strategy for oriented design and synthesis of MOF-based composites with high efficiency for various gas separation processes.