The invention discloses a one-by-one drilling empty hole grouting hole forming method and application for an advance pipe shed in a pebble accumulation layer tunnel. Pipe shed hole positions close toone another are organized into one group, drilling is conducted on a hole position in the middle of the group of pipe shed hole positions firstly, when drilling cannot be conducted because problems ofhole collapse, drill bit blocking or air leakage occur, empty hole grouting is conducted on a hole-formed section by utilizing a grouting pipe, the hole bottom of the hole-formed section and surrounding rocks around the hole wall are solidified, thus first-time drilling is completed, and first-time drilling of adjacent hole positions is completed one by one by adopting the same mode; and second-time drilling of each hole position is completed one by one by adopting the mode being the same as the first-time drilling till a hole is drilled to reach a designed depth. The one-by-one drilling empty hole grouting hole forming method can ensure the pipe shed construction quality of advance supporting of the pipe shed in a pebble stratum, and the construction process is simplified.