The enterococcus faecium were pre-fermented encapsulated by the method of emulsion and internal gelation and post-fermented encapsulated by spraying dry. The stress resistance of the both microencapsulation formulations to the storage, high temperature, gastric juice and intestinal juice were evaluated compared with free enterococcus faecium. The results showed that the survival rates of pre-fermented encapsulated enterococcus faecium were 19.46% and 6.90% higher respectively than those of un-capsulated and post-fermented encapsulated enterococcus faecium after storage at room temperature for five months. The resistance of enterococcus faecium to the high temperature at 110 ℃ and 130 ℃ was significantly increased (P＜0.05) by the pre- fermented encapsulation compared with post-fermented encapsulation and free. The survival rates of pre-fermented encapsulated and post-fermented encapsulated enterococcus faecium were significantly increased (P＜0.05) compared with those of uncoated ones when they were treated in the simulated gastric conditions for 30, 90 and 180 min. The pre-fermented encapsulated was particularly evident. The results were similar in mimic environments of gastric juice and intestinal juice. The survival rates of pre-fermented encapsulated and post-fermented encapsulated enterococcus faecium were increased 19.17% and 14.18%（P＜0.05）compared with un-capsulated ones after they were treated in the simulated intestinal conditions for 180 min.These results suggest that the resistance of encapsulated enterococcus faecium is much higher than that of un-capsulated ones. The pre- fermented encapsulation can be a more effective way than post-fermented encapsulation for protecting probiotic microbes and has a high value of practical application.