The Raman spectroscopy of pharmaceutical cocrystals based on caffeine and oxalic acid in nanosized pores of mesoporous silica has been demonstrated at various molar amounts. The Raman peak shifts of caffeine molecules express the existence of pharmaceutical cocrystals in mesoporous silica. The molar amount dependence of the peak shifts describes that caffeine and oxalic acid cocrystallized on the surface of the nanosized pores and piled up layer by layer. This is the first report that shows the Raman spectroscopy is a powerful tool to observe the synthesis of pharmaceutical cocrystals incorporated in the nanosized pores of mesoporous silica. The results indicate a way to control the size of cocrystals on a nanometer scale, which will provide higher bioavailability of pharmaceuticals.