In order to study the application effect of microbial fertilizer and compound fertilizer mixed application on microirrigation apple, three types of fertilizers were applied in spring which were urea(CK, 15 kg/plant), microbial fertilizer(5.0 kg/plant),microbial fertilizer and compound fertilizer mixed(each 2.5 kg/plant) to study the effect of different fertilizer treatments on yield, fruit quality, flowering and fruit setting of Xinshijie apple. The results showed that application of microbial fertilizer could increase the yield, fruit weight and fruit shape index, significantly increase the flowering rates and inflorescence fruit setting rate of following year, while reduce the fruit hardness and soluble solids content, and the effect of microbial fertilizer and compound fertilizer mixed application on increasing fruit weight and yield was higher than that of microbial fertilizer separate application, the effect of the two was not obvious in other aspects. Therefore, microbial fertilizer could be used instead of some chemical fertilizer and organic fertilizer in apple production to reach the aim of increasing yield and efficiency, and the effect of microbial fertilizer and compound fertilizer mixed application was best.