The invention belongs to the field of functional materials, and particularly relates to a fluorine-containing near-infrared absorption conjugated polymer and a preparation method thereof. The preparation method comprises the following steps: firstly, preparing a 3, 6-bis (5-bromothiophene-2-yl)-2, 5-bis (alkyl) pyrrolo [3, 4-c] pyrrole-1, 4-diketone monomer, then preparing dibromo fluorine-containing fluorene, and finally, reacting the 3, 6-bis (5-bromothiophene-2-yl)-2, 5-bis (alkyl) pyrrolo [3, 4-c] pyrrole-1, 4-diketone monomer with the dibromo fluorine-containing fluorene to prepare the fluorine-containing fluorene dibromo fluorine-containing fluorene. The preparation method comprises the following steps: dissolving a 1, 4-diketone monomer, dibromo fluorine-containing fluorene, a bis (trimethyltin) compound, tris (dibenzylideneacetone) dipalladium and tris (o-tolyl) phosphine in toluene, and reacting at 110 DEG C for 48 hours in an inert gas atmosphere to obtain the fluorine-containing fluorene and diketopyrrolopyrrole copolymer. The fluorine-containing fluorene and diketopyrrolopyrrole copolymer disclosed by the invention has strong absorption in a near-infrared region, and contains a perfluoro side chain, so that the efficiency of generated singlet oxygen is higher, and the photodynamic therapy efficiency can be improved.