A novel poly(4-iodobutoxylmethylsiloxane) (PIBMS) water repellent with high reaction activity was synthesized using poly(hydromethylsiloxane) (PHMS), methyl iodide (MeI) and tetrahydrofuran (THF) in the presence of a catalytic amount of PdCl2. The new chemical active group of PIBMS could covalently bond to the cotton fabric. It is conducive to improve the washability of treated cotton fabric. The structure of PIBMS was confirmed by the FT-IR and 1H NMR spectra. The PIBMS was applied onto cotton fabric by a pad-dry-cure process. PIBMS was applied to cotton fabrics and the effect of the process parameters on water repellent performance was studied. The morphology of PIBMS polymer film on the cotton fabric was investigated by SEM. The water repellency of treated cotton fabrics before and after vigorous washes was compared. The results show that the water repellent grade of cotton fabric treated with PIBMS was 90. The contact angle of the treated cotton fabric was 136.94°, which was higher than that of the untreated cotton fabric. The water repellent grade of treated cotton fabric was still as high as 80 after 20 times washing. The tear strength and the tensile strength of cotton fabric significantly increased after PIBMS treatment. The air permeability and the water vapor permeability of treated cotton fabric were slightly lower than those of untreated cotton fabrics.