Extra-deep concrete cut-off wall with depth over 60 m has been used for the reinforcement of dangerous earth-rock dams in China. The stress of cutoff wall is complex and changeable due to reservoir water level fluctuation, slope loading effect, the embedded condition of bedrock as well as the characteristic of wall materials. In this paper, the deformation and stress of concrete cut-off wall in dam body are analyzed by 3D simulation based on Shen Zhujiang’s Double Yield Surface Model in association with Biot’s consolidation theory. The hazard elimination and reinforcement project of Hualiangting reservoir dam is taken as a case study. Results reveal that the impact of the old dam reinforcement and the rising of water level exert small influence on the concrete cut-off wall. We recommend to enhancing compressive strength and reducing elastic modulus in order to meet the requirements for stress and durability; due to stress increment at the bottom of cut-off wall, we also recommend additional reinforcement for concrete cut-off wall of non-linear dam.