High pressure water inrush occurred to shaft No. 1 (auxiliary shaft) construction of Gaoligongshan Tunnel and the shaft was flooded. In this paper, the causes for the water inrush are analyzed based on strata characteristics and construction situation; and then 3 sealing schemes, i.e. underwater concrete sealing, grouting under hydrostatic pressure and combined sealing of modified cement slurry waterstop layer and grouting stone sealing layer, are proposed by comparing with shaft sealing experience of relevant industry; finally, the construction control technology is introduced, and the sealing effect is verified by pumping and drainage construction. The treatment results show that: (1) The sealing scheme that combined modified cement slurry waterstop layer and grouting stone sealing layer is selected; and the parameter design of modified cement slurry waterstop layer, the slurry waterstop layer construction technology and the cement slurry mixing proportion of the selected scheme can meet the sealing requirement of water inrush in deep and large vertical shaft. (2) The deepwater pressure camera can monitor the construction process effectively, and the sealing effect can be checked accurately by controlled water drainage. (3) The sealing effect of modified cement slurry waterstop layer with thickness of 50 m is good, reaching 99% sealing rate.