Mesoporous molecular sieve MCM-41 and zeolite-P were synthesized from natural clinoptilolite zeolite and cetyltrimethylammonium bromide under hydrothermal conditions in alkaline media. The formation path of MCM-41 and zeolite-P from natural clinoptilolite was investigated using XRD, TG, SEM, and FT-IR for the samples obtained in the course of the synthesis. XRD and TG results exhibited that in the first stage where the mixture of clinoptilolite and cetyltrimethylammonium bromide was treated in alkaline media at ambient temperature, crystal structure of clinoptilolite did not change significantly. In the second stage where the mixture was subsequently treated under hydrothermal conditions, dissolution of clinoptilolite and formation of zeolite-P were observed, while mesophase with 2d hexagonal structure of MCM-41 was not detected. In the third stage, mesostructure with 2d hexagonal symmetry was gradually formed by the adjustment of pH of the reaction mixture between 10.5 and 8.5. Structural integrity of 2d hexagonal assembly of as-synthesized MCM-41 was improved by controlling pH of the reaction mixture to 8.5 followed by the hydrothermal treatment. In contrast, the structure of zeolite-P was not affected by these treatments. SEM images of the samples showed that small particles of MCM-41 were mainly formed on the surface of the zeolite-P particles and agglomerated to larger grains. Judging from the results of XRD patterns and FT-IR spectra of the samples, it is indicated that smaller crystallites or building units of clinoptilolite that were X-ray amorphous and IR detectable were probably incorporated in the pore walls of MCM-41.