Understanding the interaction between chitosan and surfactant cetyltrimethylammonium bromide (CTAB) is fundamental to prepare nanoparticles for drug delivery but also to synthesize porous functionalized materials. In this work, we first studied the self-aggregation property of chitosan and found that the microporous structure of chitosan-templated silica was dependent on the chitosan concentration and the deacetylation degree of chitosan. The interactions between chitosan and CTAB were studied by reflection-absorption infrared spectra, which illustrate that the molecular orientations of chitosan are greatly affected by adding CTAB especially at lower pH. Through measurements of the critical micelle concentration values of CTAB and characterizations of porous structures, it is indicated that micro-meso silica can be synthesized with the chitosan-CTAB hybrid, and both surface area and pore volume as well as the meso-periodity of silica can be modulated by adding CTAB in the sol-gel synthesis process at proper pH value.