The invention relates to a method for improving the laying flatness of a sand quilt of a geotextiles-laying vessel in a stormy wave deepwater area. The method is characterized by comprising the following steps of (1) manufacturing a sand quilt bag; (2) winding the sand quilt bag on the geotextiles-laying vessel; (3) enabling the geotextiles-laying vessel to arrive in place; (4) conducting fillingand laying on the sand quilt bag, wherein firstly, a first longitudinal partition cabin is arranged in a driving mode; a winding drum is started to enable the sand quilt bag to drop slowly; when the sand quilt bag touches the ground, the winding drum is started to enable the sand quilt bag to slide down while the vessel is moved in parallel, and the vessel is moved by 2-3 m every time; when a second partition cabin arrives at a sliding plate, the other two mud pumps conduct filling on the second longitudinal partition cabin through sand delivery pipes; the mud pumps are started to fill sand into the sand quilt bag through all sleeve openings; the sand filling volume is calculated according to the sand filling time, so that the filling thickness is controlled; the process is repeated untilthe sand quilt bag is laid completely. Through the technical scheme, the longitudinal partition cabin type filling bag is filled with sand and is arranged in a driven mode, the overall flatness can begreatly improved, and the strength of a bag body can be enhanced. Meanwhile, the cost is lowered, and the production efficiency is improved.