In this work, silicone softener (PTSO-PEG) was synthesized, with piperazine terminated polydimethylsiloxane (PTSO) and epoxy terminated polyethylene glycol (EPEG) as raw materials. Chemical structure of PTSO-PEG was characterized by (1)H NMR, FTIR, GPC, and TGA. Its application on cotton fabrics was studied. Morphologies of silicone modified surfaces on cotton fabrics and silicon wafers were investigated by SEM and AFM, respectively. The morphology images indicated that PTSO-PEG treated surface was macroscopically smooth and microscopically rough. Performance properties of silicone treated cotton fabrics, including hydrophilicity, whiteness, and softness, were tested. The results showed that PTSO-PEG treated cotton fabrics expressed better whiteness and hydrophilicity than traditional amino silicone treated sample. The piperazine and hydrophilic polyether groups on PTSO-PEG molecules disturbed the continuous and orderly arrangement of Si-CH3 groups, giving the cotton a hydrophilic and rough surface. This work provided a cost-effective and environmental method to synthesize and apply high performance silicone softener.