Abstract: The authors used 3 kinds of microbial fertilizers (YBGJ, EM, MMJ) to study their effects on watermelon roots. The results showed that after the application of three microbial fertilizers, the growth of watermelon was promoted, there was significant difference among the three treatments on the morbidity of seedlings (P <0.01), YBGJ could effectively decrease the morbidity of wilt and had the best effect; after 1 year of the application of EM, the morbidity of watermelon root and stem decreased, after the application of YBGJ, the morbidity of leaf decreased and morbidity of clubroot decreased. There was no significant difference among the treatments on the yield (P >0.05), treatment YBGJ had better effect on yield, the order was YBGJ＞EM＞ MMJ＞CK. After the use of microbial fertilizers, survival rate, morbidity and yield were all improved compared with those of CK, the use of microbial fertilizer on vegetable in greenhouse should be suggested.