In methanol-aqueous solutions, three novel structure-directing agents (SDAs) were generated in situ and presented. These in situ reactions feature N-methylation transformations between CH3OH solvent and organic cyclic aliphatic and aromatic amines, i.e. 2-methylpiperazine, 1,4-diazabicyclo[2,2,2]octane (dabco) and 3-(aminomethyl)pyridine. Distinct from conventional Eschweiler-Clarke methylation containing excess formic acid and formaldehyde, such a direct methylation transformation from methanol molecules is unique. In the presence of new SDAs, three organically templated zinc phosphites/phosphates, [pmpip][Zn3(HPO3)4] I (pmpip = N,N,N',N'-tetramethyl-2-methylpiperazinium), [dmdabco][Zn3(HPO3)4] II (dmdabco = N,N'-dimethyl-1,4-diazabicyclo[2,2,2]octane) and [Hmampy][Zn2(HPO4)3] III (mampy = N-methyl-3-(aminomethyl)pyridine), have been prepared and structurally characterized by elemental analysis, IR, thermogravimetric analysis, powder and single-crystal X-ray diffraction. Compound I exhibits a 2D layer with eight-membered apertures, compounds II and III possess a 3D interrupted framework with intersecting 8-, 10- and 12-ring channels (for II), and 8-, 10-ring channels (for III), respectively.