There is an increasing desire to use natural products that will be both effective and biodegradable. The aim of this work is to investigate the effect of modifying flax fibers with silicon compounds (silanes and polysiloxanes), as well as examining the effect of the mercerization process on their properties. Two types of polysiloxanes have been synthesized and confirmed by infrared spectroscopy (FTIR) and nuclear magnetic resonance spectroscopy (NMR). Scanning electron microscopy (SEM), FTIR, thermogravimetry analysis (TGA) and pyrolysis-combustion flow calorimetry (PCFC) tests of the fibers were performed. On the SEM pictures, flax fibers purified and covered with silanes were visible after treatment. FTIR analysis showed stable bonds between the fibers and the silicon compounds. Promising results of thermal stability were obtained. It was also found that modification had a positive effect on the flammability. The conducted research showed that the use of such modifications, in the context of using flax fibers for composites, can yield very good results.