The invention relates to a preparation method of a defoaming agent for a waterborne 
system. The preparation method of the defoaming agent for the waterborne 
system comprises the following steps: a) adding 
silicon oil, gaseous 
silicon dioxide and catalyst into a reaction container according to proportions, and preparing 
silicon cream under an agitating condition protected by 
nitrogen; b) adding 
hydrogen-containing silicon oil and allyl polyether into the reaction container, agitating under the protection of 
nitrogen, increasing temperature and adding an initiator for reaction to obtain polyether modified organic silicon; c) jading the silicon cream obtained in step a), the polyether modified organic silicon obtained in step b) and an emulsifier into the reaction container, adding water for emulsification under a high-speed agitating condition, and adding a 
thickening agent to regulate 
viscosity to obtain a product. The defoaming agent prepared by adopting the preparation method provided by the invention has the advantages that the 
active components are low, the manufacturing cost is low and the environmental friendliness is better; the emulsification is stable, the compatibility in the waterborne 
system is good, the defoaming agent is easy to disperse, the 
surface tension is low, the defoaming speed is quick, the foam inhibiting time is long, the 
thermal resistance, 
shear resistance and acid and alkali resistance thereof are good, and the defoaming agent can adapt to various places; the defoaming agent can be separately used and can also be jointly used with other adjuvants, the stability is good, the phenomenon of oil floating due to demulsification does not occur, no 
sediment is produced and shrinkage cavities during 
coating are not caused; and the defoaming agent is also very effective to non-waterborne systems.