Objective To observe the efficacy of electroacupuncture(EA) on the acupoint combination of He-(sea) points, front-mu points, and shu-points(abbrev. He-Mu-Shu) for the treatment of functional diarrhea, and to explore the effect of He-Mu-Shu point combination EA on the anxiety of patients. Methods A randomized controlled clinical trial was performed in 62 functional diarrhea patients. All of the patients were randomly divided into He-Mu-Shu group(32 cases) and medicine group(30 cases). He-Mu-Shu group was treated with EA on unilateral Quchi, Shangjuxu, Tianshu, Dachangshu point alternatively, and medicine group was treated with oral use of Loperamide hydrochloride capsules. Both groups were treated for 4 continuous weeks. Defecation frequency, stool property and anxiety scores were observed before treatment and 2, 4 weeks after treatment. Results After treatment, weekly defecation frequency, stool property and anxiety scores were improved in both groups, and the differences were statistically significant compared with those before treatment(P < 0.05). He-Mu-Shu point combination EA had better effect on improving weekly defecation frequency, stool property and anxiety scores of functional diarrhea patients than Loperamide hydrochloride capsules, and the differences were statistically significant (P < 0.05). Conclusion The clinical efficacy and anxiety-relief action of He-Mu-Shu point combination EA on functional diarrhea are superior to oral use of Loperamide hydrochloride capsules.