We have compared the structure, phase transitions and the thermal motion mechanisms of the undecylenic acid in bulk and inside a porous matrix using powder X-ray diffraction, calorimetry and IR-spectroscopy methods. The matrix used was a porous silicon with cylindrical pores (D = 20 nm). The interaction between the walls of the porous silicon and the nanocrystals of the undecylenic acid results in a crystalline structure, which is significantly different from the structure of bulk undecylenic acid. A phase transition in the wall-adjacent layer of the undecylenic acid nanocrystals was shown to take place. The solid-state phase transition temperatures, as well as the melting point, were shown to be lower for nanocrystals. Topological soliton motion mechanism was suggested to explain the thermal motion of the undecylenic acid molecules in the rotator phase.