The invention relates to a method for preparing a paper-based copper clad laminate. The method comprises the following steps: 1) uniformly mixing a PBAT raw material, an inorganic heat conductive filler and a flame retardant to obtain a mixture, and conveying the mixture to a material storage bin of a laminating machine; 2) carrying out single-sided lamination: placing the mixture in the laminating machine, carrying out lamination on a single side of bleached wood pulp paper, and cooling to obtain single-sided laminated bleached wood pulp paper; 3) carrying out double-sided lamination: controlling the laminating machine to cladding the mixture onto the other side of the bleached wood pulp paper, and cooling to obtain double-sided laminated bleached wood pulp paper, namely insulating material sheets; and 4) taking and superimposing a plurality of insulating material sheets, cladding a copper foil on a single side or double sides after superimposing, and carrying out vacuum thermocompression to obtain the paper-based copper clad laminate. The method provided by the invention adopts a laminating way to replace a glue coating way to obtain the insulating sheets of the paper-based copper clad laminate, thereby saving a large number of process steps and organic reagents, and being environmentally-friendly and low in production cost. The prepared paper-based copper clad laminate has the advantages of flame retardance of Fv0 grade, low water absorption rate, good punching property and solderability resistance, and the like.