In this study, we fabricated the multifunctional fluorophenyl polysiloxane coatings with different grafting densities of fluorophenyl groups. The structure and emulsion stability of fluorophenyl polysiloxanes were analyzed by Fourier-transform infrared (FT-IR) spectrum, nuclear magnetic resonance, particle size, and zeta potential, and the application performance of fluorophenyl polysiloxanes were investigated. FT-IR spectroscopy, X-ray photoelectron spectroscopy, and scanning electron microscopy proved the successful application of fluorophenyl polysiloxanes onto cotton fabrics. Afterwards, the liquid repellency, thermal stability, and deepening performance of cotton fabrics treated with fluorophenyl polysiloxane coatings were investigated. Results showed that all the treated cotton fabrics possessed contact angles greater than 110 , and cotton fabrics treated with FPPS-23 (fluorophenyl polysiloxane with 23% theoretical fluorine content) obtained the best thermal stability. Additionally, the blue cotton fabric and orange cotton fabric treated with FPPS-23 had the best deepening performance with K/S values as 27.23 and 20.56, which increased by 34.20% and 16.82%, respectively.