Molecular selective adsorption of alkylphenols and alkylanilines onto n-alkyl grafted MCM-41 with different alkyl chain lengths and Al contents was studied. Octyl groups gave better adsorbent performance than pentyl and dodecyl groups. Nitrogen and water adsorption isotherms revealed that the octyl-grafted sample has a large volume of strongly hydrophobic nanospaces between the grafted alkyl chains. Octyl-grafted MCM-41 adsorbed alkylphenols from aqueous solutions with high molecular selectivity: Nonylphenol, an endocrine disrupter, is efficiently removed by adsorption onto n-octyl grafted MCM-41, while adsorption of t-amylphenol is small and that of phenol is undetectable. Comparison of molecular selectivities for alkylphenols and alkylanilines reveals that hydrophilic and hydrophobic groups on molecules independently affect the selectivity. Infrared spectra of n-heptylaniline captured in the adsorbent show that the amino groups are strongly hydrogen-bonded to silanol groups on the inorganic pore walls: The molecules fit into the organic–inorganic nanostructure, interacting with the inorganic walls as well as the organic moiety. Since the amounts of Al that could be doped into MCM-41 were much lower than the adsorption amounts of the 4-nonylphenol and 4-n-heptylaniline, changes in the adsorption amounts due to the formation of acidic sites by Al doping could not be clearly observed. It was concluded that a large volume of highly hydrophobic nanospaces surrounded by ionic inorganic walls was important for efficient adsorption of these molecules.