The invention relates to an underwater super-deep shield originating/lifting-out well structure and a construction method thereof. An originating/lifting-out well is arranged in water, the upper portion of the originating/lifting-out well is a soft stratum part, and the lower portion of the originating/lifting-out well is a hard rock stratum part. A well body of the soft stratum part comprises an enclosure wall, the interior of the enclosure wall is a lining wall, and the lining wall is provided with a plurality of transverse annular frame beams from top to bottom. A well body of the hard rock stratum part comprises an ejector anchor protection system, and the interior of the ejector anchor protection system is a lining wall. A shield tunnel portal is located at the bottom of the well body of the hard rock stratum part. The underwater super-deep shield originating/lifting-out well structure is good in structural stability, high in safety and high in water leakage prevention performance, a well body structure is arranged by combining actual geologic conditions, the construction progress is accelerated, the construction space and the hoisting space are good, and the difficult problem of construction of the originating/lifting-out well in a water area complex environment and a flow-interrupted unallowed river/riverway can be solved.