A method for manufacturing a polyimide composite film for a flexible metal-clad substrate includes the following steps, providing a polyamide acid solution; providing fluorine polymer particles and mixing the fluorine polymer particles with a dispersant and an organic solution to prepare a fluorine polymer particle dispersion; forming a colloidal polyimide film from the polyamide acid solution; and coating the colloidal polyimide film with the fluorine polymer particle dispersion and then performing baking to form a polyimide composite film.