The maximum depth of the excavation in No. 5 well of a scientific device project is 45.45 m, which is currently the deepest non-circular excavation project in Shanghai. The implementation of the project encountered many challenges and new technical problems, and relevant technological breakthroughs are achieved. Such as, the double-layer curtain design scheme combining deep wall and shallow curtain was adopted to control the safety risk caused by the leakage of the ultra-deep excavation in soft soil. The world’s deepest TRD water-proof curtain with a depth of 69m was first successfully applied in the excavation project. And the ex-situ field trial wall test of TRD cement-soil mixing walls with a depth of 86m and a thickness of 1.10 m was carried out and completed for the first time. Based on the successfully implemented of No. 5 well project, the design and practice of the 45m-level extreme-deep excavation in Shanghai soft soil area was introduced. Including the overall design scheme, ultra-deep diaphragm wall design, ultra-deep TRD waterproof curtain design and ex-situ wall test, precipitation design and groundwater control effect of multiple aquifers, and project implementation effect. The successful design and implementation of this project can provide reference for the similar projects.