A novel polysiloxane bearing dodecyl and epoxy side groups (DESO) was synthesized as an intermediate through hydrosilylation of polymethylhydrosiloxane with allyl glycidyl ether and 1-dodecene. Then, dodecyl/piperazine functional polysiloxane (DPSO) was prepared through the reaction of N-aminoethylpiperazine with DESO. The chemical structure of DPSO was characterized with FTIR and 1 H-NMR spectroscopy and its application performance on cotton fabrics was studied. DPSO with dodecyl side groups gifted the treated fabrics with good wettability and whiteness compared with piperazine functional polysiloxane, while with a slightly reduced softness as well as thickening handle. Film morphology, orientation, and performance on cotton substrates of DPSO were investigated by scanning electron microscope, atomic force microscopy, X-ray photoelectron microscope, and so on. Affected by the dodecyl side groups, DPSO formed relatively hydrophilic, macroscopically smooth but actually uneven films with many dodecyl side chain pillars on the treated substrate surfaces.