The present invention discloses a multifunctional biological compound fertilizer as well as a preparation method and an application thereof. The multifunctional biological compound fertilizer contains 18-20g*kg<-1> of organic matters, 0.2-0.5 hundred million CFU*g<-1> of total functional bacillus, 40 to 50g*kg<-1> of total N(N), 20-30g*kg<-1> of total P(P2O5) and 50-60g*kg<-1> of total K(K2O). The biological compound fertilizer is prepared by adopting rotten and dried organic fertilizer as an absorbing carrier, providing a good environment for storing and playing effect of the bacillus with specific functions and adding a small amount of fertilizer on the basis of the good environment. The multifunctional biological compound fertilizer integrates the advantages of organic fertilizer, microbial inoculum and fertilizer, and remains a large amount of beneficial microorganism. The multifunctional biological compound fertilizer has obvious effects of increasing production and yield when being applied in vegetables and grain crops, has effects to the crops of the season, has obvious promoting effects to the crop of the second season, has the effects of optimizing the microbial structures in soil and improving the ecological quality, can solve continuous cropping and soil with problems and belongs to an environment-friendly fertilizer.