The invention discloses a method for the modeling production of fusion protein by utilizing the trans-splicing of intein, which can be used in fields, such as gene engineering, enzyme production, medicine production, food industry, farming and animal industry, and the like. In the invention, A target protein part with special biological functions and auxiliary protein with general functions are mainly connected together by utilizing the trans-splicing of the intein so as to obtain the fusion protein; the target protein T, the auxiliary protein P1 and P2, the intein A and the intein B which are mutually incompatible (such as blue algae: DnaE and DnaB of Synechocystis sp. PCC6803) are selected; the intein A and intein B are respectively decomposed into an amino terminal (N terminal) and a carboxyl terminal (C terminal), i.e. An, Ac, Bn and Bc; after different carrier systems are constructed; protein segments Ac-T-Bn, P1-An, Bc-P2, An and Bc are respectively obtained through host expression; the obtained protein segments are mixed; and the trans-splicing of the intein is carried out to generate the fusion protein P1-T-P2, P1-T or T-P2.