For solving the problem that a large amount of air bubbles are generated in an organism aerobic batch cultivation process, the invention, based on the knowledge of microorganism growth kinetics and micro ecological kinetics, develops an active defoaming method for controlling foam generation. Obviously differing from the passive defoaming method or foam end control methods represented by defoamers and defoaming devices, the method effectively controls the generation of foam by allowing part of mixed liquid in an original building to run in the traditional inlet and outlet water pipes in a backflow and circulation mode, namely a fake continuous running mode, and by controlling parameters such a backflow speed and an upflow speed in a reaction structure. The method avoids using a defoamer or defoaming device and polluting culture liquid with the defoamer, retains the structure of the original structure, saves investment cost to a maximum degree, and meets the requirements for cost-effect combination and low operation cost in actual operation. The method is mainly suitable to be used for removing foam generated in a sludge batch aerobic culture process in the field of waste water biological treatment and an aerobic batch fermentation process in the field of biological fermentation.