The invention discloses a separate mining, separate transporting and filling mining system and method for coal gangue of a low coal seam. The system comprises a filling support, wherein a filling scraper conveyer is arranged at the rear end of the filling support, a supporting plate capable of extending forwards is arranged below the front end of a top beam of the filling support, a coal mining machine and a working face scraper conveyer are arranged below the filling support, and the working face scraper conveyer is in overlap joint/connection with a gate roadway adhesive tape in an adhesivetape delivery gate roadway, and is further in overlap joint/connection with the filling scraper conveyer arranged at the rear end of the filling support. According to the separate mining, separate transporting and filling mining system and method for the coal gangue of the low coal seam, separate mining and separate transporting of the coal gangue is realized, and the problem of large difficulty in parallel mining and filling work is solved, so that the washing and treatment cost of the gangue is reduced. The invention further relates to a separate mining, separate transporting and filling mining system and method for the coal gangue of the low coal seam.