This paper reports a one-pot sol–gel approach for the synthesis of the alkylammonium-functionalized mesoporous silica particles with hollow structures and mesoporous silica films via hydrothermal reaction through the self-assembly of N-trimethoxysilylpropyl-N,N,N-trimethylammonium chloride (TMAPS) and tetraethoxysilane (TEOS) as a silica source, dodecyldimethyl(3-sulfopropyl)ammonium hydroxide (DDAPS) and fluorocarbon anion (ammonium perfluorooctanoate (APFO)) as the structure-directing agent. The alkylammonium-functionalized hollow mesoporous silica particles exhibited a different morphology, mesoporosity, and hollow structure with a layered mesostructure in the shell according to the DDAPS/APFO surfactant molar ratios (DDAPS/APFO = 3/1~1/9 or APFO in the range of 10~80 mM), reaction times (6~48 h), and reaction temperatures (45~95 °C). Alkylammonium-functionalized hollow mesoporous silica particles with spherical morphologies were produced from precipitation in the bottom of the reaction bottle after the hydrothermal reaction. At a DDAPS/APFO surfactant ratio of 1/3, reaction temperature of 60 °C, and reaction times of 24 h and 48 h, the alkylammonium-functionalized hollow mesoporous silica spheres displayed a multilayered mesostructure in the shell. The sphere size could be controlled from ca. 76 nm to ca. 350 nm with a shell thickness of ca. 35 nm. In addition, alkylammonium-functionalized mesoporous silica films were produced at the air–water interface, whereas hollow mesoporous silica spheres were produced with precipitation in the bottom of the reaction bottle. The film thickness was controlled from ca. 210 nm to ca. 400 nm.