A side amino polysiloxane-modified polyurethane coating agent is disclosed. Side aminopolysiloxane (SAPDMS), polytetrahydrofuran glycol and polyethylene glycol as mixed soft segments, dimethylol propionic acid as a hydrophilic chain extender, and 1,4-butanediol as a hard segment regulator are reacted with isophorone diisocyanate to synthesize a waterborne silicone modified polyurethane (WSSPU), and the waterproof and moisture-permeable fabric coating agent is prepared based on the WSSPU. The composition and microstructure of a WSSPU film can be characterized by an infrared spectroscopy, a differential scanning calorimeter, a dynamic mechanical analyzer, a positron annihilation lifetime spectroscopy, and the like. The mechanical properties of the WSSPU film and the waterproof and moisture-permeable properties of a coated fabric are investigated. Results show that a stable emulsion can be obtained when the dosage of the side aminopolysiloxane (mass ratio) is less than 15%. After polysiloxane modification, the internal micro-phase separation structure of the film is more obvious, the free volume cavity becomes larger, and the moisture-permeable properties are improved.