In this work, spherical amine-functionalized mesoporous silica (Sp-Amino-Si) molecular sieve was fabricated by an acid hydrothermal method using 3-aminopropyltriethoxysilane as a modifier and toluene as the solvent. The results of scanning electron microscopy, Barrett-Joyner-Halenda pore size distribution, Fourier transform-infrared spectroscopy, and low-angle X-ray diffraction patterns revealed that the Sp-Amino-Si was monodispersed microspheres with uniform and controllable pore sizes sharing two-dimensional hexagonal P6mm symmetry and a large number of amino groups. The Sp-Amino-Si molecular sieve was verified to be suitable for the selective separation of aromatic hydrocarbons (AMHs) containing two fused benzene rings among other compounds from environmental water matrix. Under the optimized conditions, the Sp-Amino-Si exhibited much higher adsorption efficiency for AMHs (above 88.19%), comparing to the original SBA-15 (below 44.52%). The maximum adsorption capacities for naphthalene, methyl naphthalene, 2-methyl naphthalene, and acenaphthene were 477.1, 1006.5, 893.3, and 1253.2 µg·g−1, respectively. The high selectivity of Sp-Amino-Si for the four AMHs attributed to the size sieving and p-π interactions between the lone pair electrons of amine groups and the π-electrons in AMHs molecules. The Sp-Amino-Si based solid-phase extraction coupled with high performance liquid chromatography detection method was constructed for the analysis of the four AMHs, and the recoveries of spiked AMHs ranged from 89.67% to 112.74% with a relative standard deviation lower than 5.75%. This study provides some inspiration and a reliable method for AMHs separation, removal, and analysis.