The invention discloses an organic silicon softening agent used with a fluorine series waterproof agent in the same bath and a preparation method thereof. The preparation method comprises the following steps: firstly, enabling isocyanate ethyl acrylate and long-carbon-chain fatty alcohol to react, so as to prepare an unsaturated polyurethane acrylate long-carbon-chain monomer UPLCM; then adding the UPLCM monomer and allyl epoxy polyether into hydrogen-containing silicone oil PHMS (Polymethylhydrosiloxane) according to a ratio and raising the temperature to 60 to 90 DEG C; after adding a chloroplatinic acid catalyst and reacting for 2 to 10h, decompressing and distilling to remove a low-boiling-point substance, so as to obtain co-modified silicone oil; then dissolving tetramethyl hexanediamine acetate and the co-modified silicone oil into an organic solvent according to a ratio and reacting at the temperature of 70 to 100 DEG C for 1 to 20h; and finally, emulsifying the silicone oil under the action of a compound emulsifying agent, so as to obtain the organic silicon softening agent for use with the fluorine series waterproof agent in the same bath. The preparation method disclosedby the invention is simple and the prepared softening agent can be used for improving the hand feeling of textiles; and meanwhile, the performance of the waterproof agent is not reduced and the softening agent is convenient to use.