The invention discloses a preparation method and application of a double-target fusion protein, and belongs to the technical field of medicines. Compared with wild type FGF19 and GLP-1, the novel fusion protein obtained by transforming an FGF19 sequence and fusing the FGF19 sequence with GLP-1 has a more long-acting and more stable effect, further reduces the carcinogenic risk of FGF19, can better improve liver injury and correct metabolic disorder, obesity, overweight, metabolic syndrome, diabetes, dyslipidemia and other diseases. In addition, in the treatment process, the side effect of gastrointestinal discomfort such as diet decline caused by GLP-1 treatment does not occur, and wide application prospects are achieved.