To address the engineering challenges posed by large deformations of surrounding rock, cracking of primary support, rockfall collapse, surface settlement, and slow construction progress in long-distance water diversion tunnels through extremely soft rock formations, a case study is conducted on the Adit #12-1 of the Yangtze River-to-Hanjiang River Water Diversion Project. Focusing on carbonaceous shale strata with uniaxial compressive strength below 5 MPa, an integrated approach combining 3DEC discrete element numerical simulation, field monitoring, and engineering practice are employed to systematically analyze the spatiotemporal evolution of large deformations during tunnel excavation in extremely soft rock. The results reveal that the surrounding rock experiences significant early-stage deformation, primarily concentrated within 1 to 4 days after upper bench excavation. By implementing a three-bench excavation method with temporary invert closure and vertical struts, the deformation convergence time can be reduced to 12 days while minimizing deformation magnitude through enhanced arching effects. Based on these findings, a threestage control strategy is proposed: advance reinforcement using 108 mm pipe roofing combined with 42 mm grouted spiles; implementation of a “three-bench + vertical struts + dual temporary inverts” excavation method; and timely installation of steel ribs and shotcrete support. This approach has demonstrated excellent application results in Adit #12-1. Following the completion of primary support, settlement deformation stabilized, with subsequent monitoring measurements remaining within 20 mm.