For improving the yield of exopolysaccharides (EPSs) produced by Cordyceps militaris and the efficiency of downstream separation technology, a combination technology of repeated batch fermentation and two-stage foam fractionation was designed. First, the suitable parameters of repeated batch fermentation (RBF) were determined. The results showed that the suitable broth replacement time point and replacement ratio were fifth day and 80% (v/v), respectively. The fermentation of Cordyceps militaris was performed for five cycles without a significant loss of fermentability, and the fermenting time decreased from 25 days to 13 days through RBF strategy. Then, the replacement broth was used as the feeding solution of foam fractionation. The effects of mycelia, tween 80 and volumetric air flowrate on the performance of foam fractionation were investigated, respectively. Under the suitable operating conditions, the total enrichment ratio of EPSs in the two-stage foam fractionation reached as high as 7.12.