Conventionally, mesoporous silica nanoparticles are prepared by catalysing silicon alkoxides using acids or bases and are highly important in storage, delivery, and catalysis. Here, for the first time, we demonstrate that a transition metal ion (such as Ni(II), Co(II), and Mn(II)) also catalyses the hydrolysis and condensation reactions of silicon alkoxides in aqueous media without any additional acid or base to synthesize mesostructured and micro/mesostructured silica nanoparticles. An aqueous solution of a transition metal salt (specifically, nitrate salts of Ni(II), Co(II), or Mn(II), or chloride and sulphate salts of Ni(II)), 10-Lauryl ether (C12H25(OCH2CH2)10OH, C12E10) and cetyltrimethylammonium bromide (C16H33N(CH3)3Br, CTAB), and tetramethyl orthosilicate (TMOS) undergoes a precipitation reaction at room temperature, yielding ultra-small ordered mesostructured silica nanoparticles. These nanoparticles are subsequently calcined to produce mesoporous silica (meso-SiO2) with a high surface area (680–871 m2/g), large pore-volume (2.2–3.71 cm3/g), and small pore-size (1.2–3.0 nm). Moreover, the counter anions of the salts play an important role in the assembly process to obtain nanoparticles with an additional well-defined secondary pore (7.5–33.4 nm or larger). Coordinated water of the metal ion and methoxy group of the silica source react to produce a complex in which two hydroxy sides are in close vicinity to speed up the condensation reaction. We propose a hydrolysis and condensation reaction mechanism for TMOS to highlight the role of the metal ion as a catalyst.