The invention relates to a method and system for debugging a boiler of a 1045MW ultra-supercritical coal-fired unit through pipe purging. Cooling water pipelines of a superheater and a reheater are flushed after the boiler is subjected to cold flushing, and then the hot flushing is performed on the boiler. The boiler is controlled to heat and pressurize; a powder manufacturing system is introduced and subjected to purging test; cooling water-steam pipelines of the superheater and the reheater are flushed, and then high-pressure bypass pipelines are purged. The boiler is controlled to heat and pressurize; a first steam system and a second steam system are connected in series and subjected to pressure-reduced purging, and then the high-pressure bypass pipelines and pipe purging steam pipelines of the boiler are purged. The boiler is controlled to heat and pressurize; the first steam system and the second steam system are connected in series and subjected to pressure-reduced purging until a target plate meets the preset conditions after inspection, and then the ash purging steam pipelines of the remaining main body of the boiler and high-pressure steam inlet pipelines of small machines are purged. According to the method and system, debugging through pipe purging are performed on the 1045MW ultra-supercritical coal-fired unit, so as to avoid the potential risk of residues to the operation safety of the boiler of a steam turbogenerator set, as well as improving the use safety of the boiler of the coal-fired unit.