The invention relates to a preparing method of a polyimide composite film. The method comprises the steps that modified layered silicate is added into a polyimide prepolymer, a polyimide polymer solution is obtained through polymerization and then is smeared on a substrate, heating and curing are carried out, and the polyimide composite film is obtained, wherein amino functional groups are carried on the surface of modified layered silicate. The thermal stability of the polyimide composite film provided with the preparing method is greatly improved, the thermal decomposition temperature can be increased by 25 DEG C, the mechanical property of the polyimide composite film is greatly improved, the tensile strength can reach 113.7 MPa, and the Young modulus can be enlarged to 2536 MPa. The polyimide composite film provided with the preparing method is simple in modification process and low in modification raw material cost.