Three novel side-chain fluoroalkyl polyether oligomers with different molecular weight were synthesized base on the ring-opening polymerization of 3-perfluoro-n-butyl-1,2-epoxypropane, followed by terminal esterification using acryloyl chloride. The oligomer intermediates were used as functional monomers for emulsion copolymerization with methyl methacrylate, butyl acrylate, and hydroxyethyl methacrylate. The produced latexes were used for hydrophobic and oil-phobic finishing on cotton fabric surface and the treated cotton fabrics were tested by scanning electron microscopy and energy-dispersive spectroscopy, combined with chemical composition analysis by X-ray photoelectron spectroscopy. The result showed that fluorinated copolymers were successfully coated on the cotton fibers’ surface. Water contact angles was used to evaluate the wettability and the results showed that treated cotton fabrics possessed good hydrophobicity with the contact angle of 139.1 ± 1°, and the heat resistance of treated cotton fabrics was identified improved through the thermogravimetric analyses (TGA).