A subgrade with local deep excavation and backfilling structure and a rapid construction method thereof are provided. Supporting cast-in-place piles are laid at positions where an underground pipe gallery is located in a subgrade structure, and soil there between are longitudinally excavated to form a line-shaped foundation pit. A bottom of the line-shaped deep foundation pit is reinforced to support the underground pipe gallery, and lateral peripheral regions and top peripheral regions of the underground pipe gallery are backfilled with block geobag reinforced fillers. Geogrids are placed on the top of the underground pipe gallery, then backfilling compaction and reinforcing are performed, and the geogrids are fixedly assembled with anchor bolts. The construction method is simple and easy. By using compacted block geobag reinforced fillers and cement solidified slurry, an overall quality of the subgrade structure after backfilling can be ensured, and construction period and cost can be greatly reduced.