The invention discloses a shallow coal seam water protection mining method and an application thereof and belongs to the technical field of coal mining. In a working face, a plurality of pre-excavation roadways are vertically or obliquely demarcated from a main transportation roadway, roadway excavation is conducted in a multipoint parallel operation mode, and the excavated roadways are filled intime. By controlling the roadway excavation width, the roadway interval width, the roadway excavation speed, the filling speed and the interval filling time, the fracture development of mining overburden rock and the falling capacity of roadway roofs are effectively controlled. By means of the method, continuous, stable and efficient coal production of the working face is guaranteed, sufficient time and effective space are provided for filling of the working face so as to make a filling body solidify and meet bearing strength requirements, evolution of the permeability of a water-resisting layer on a water flowing fracture zone of a shallow coal seam is controlled effectively, water protection mining of an occurrence area of the shallow coal seam is achieved, selection and application conditions of the water protection mining method are widened, and meanwhile safe, efficient and high-recovery-rate mining of coal resources is achieved.