The anionic silicon-containing waterborne polyurethane prepolymer was prepared by introducing hydroxyl terminated silicone oil (PDMS-OH) into the polyurethane prepolymer chain segments and using dimethylol propionic acid (DMPA) as hydrophilic chain extender. The anionic silicon-containing waterborne polyurethane prepolymer was polymerized with propylene glycol diacrylate (TPGDA) to encapsulate paraffin core material, and the phase change energy storage microcapsule material of anionic silicon-containing waterborne polyurethane shell material was obtained. The effects of PDMS-OH and polyether polyol (PPG2000) on the properties of the phase change energy storage microcapsules were analyzed. The results show that PDMS-OH has been successfully incorporated into the main chains of polyurethane prepolymer, and the shell material has been successfully coated with paraffin core material. The introduction of PDMS-OH improves the mechanical strength of the shell material, and the core material encapsulation rate of the phase change energy storage microcapsules is improved. For the PU90/10 MicroPCMs, the melting enthalpy is 157.25 J/g, the crystallization enthalpy is 183.17 J/g, and the paraffin content is 75.43%. The introduction of PDMS-OH also reduces the particle size of the latex beam in the emulsion, and the minimum particle size is 181.45 nm, which greatly reduces the leakage of the microcapsule core material. In addition, with the increase of PDMS-OH / PPG2000 mole ratio, the mass loss rate of the first stage decomposition is increased, and the mass loss rate of PU90 / 10 MicroPCMs is 73.40 %, indicating that the coating ratio is further improved.