Background Rhamnolipid is the best known microbial-derived biosurfactants, which has attracted great interest as potential ‘‘green” alternative for synthetic surfactants. However, rhamnolipid is major contributor to severe foam problems, which greatly inhibits the economics of industrial-scale production. In this study, a novel foam-control system was established for ex situ dealing with the massive overflowing foam. Based on the designed facility, foam reduction efficiency, rhamnolipid production by batch and repeated fed-batch fermentation were comprehensively investigated. Results An ex situ foam-control system was developed to control the massive overflowing foam and improve rhamnolipid production. It was found that the size of individual bubble in the early stage was much larger than that of late fermentation stage and the foam liquefaction efficiency decreased from 54.37% at the beginning to only 9.23 % at the end of the fermentation. This difference of bubble stability directly resulted higher foam reduction efficiency of 67.46 % in the early stage, whereas the small uniform bubbles can only be reduced by 57.53 % at the later fermentation stage. Moreover, reduction of secondary foam is very important for foam controlling. Two improved design of the device in this study got about 20% improvement of foam reduction efficiency, respectively. The batch fermentation result showed that the average volume of the overflowing foam was reduced from 58~640 mL/min to 19~216 mL/min during fermentation process, presenting presented a notable reduction efficiency ranging from 51.92% to 73.47%. Meanwhile, rhamnolipid production of batch fermentation reached to 45.63g/L, and the yield 0.76g/g was significantly better than ever reported. Further, Moreover, a repeated fed-batch fermentation based on the overall optimization was carried out, total rhamnolipids concentration of 48.67 g/L was reached with yield around of 0.67-0.83 g/g, which presented an improvement of 62% and 49% compared with conventional batch fermentation by using various kinds of defoam, respectively. Conclusions The ex situ foam-control system presented a notable reduction efficiency, which helped a lot to easily solve the severe foaming problem without any defoamer addition. Moreover, rhamnolipid production and yield by repeated fed-batch fermentation got prominent improvement compared to conventional batch cultivation, which can further facilitate economical production of rhamnolipids at large scales.