The layout of the deep waterstop scheme of the transverse joint has a great influence on the stress of the volute part of the axial flow turbine unit, it is usually determined according to the engineering experience, and there is no unified standard. However, it is commonly recognized that an optimal layout of the waterstop scheme should not only meet the anti-seepage and safety requirement, but also have as less effect on the volute stress as possible. Based on an actual axial flow hydropower station project, the ANSYS three-dimensional finite element model of the powerhouse is established to simulate the influence of different waterstop arrangements on the volute stress under the two deep waterstop schemes of upstream closure and upstream connection under normal operation and unit maintenance conditions. Then, the stress changes of the volute inlet section, the internal typical section and the external concrete under the two deep waterstop schemes are compared and analyzed. The results show that with the rise of the waterstop position, the stress changes of the volute under the two schemes are the same; but under the same waterstop position, the upstream connection scheme has more than twice the decreased magnitude on the various stresses of the volute than the upstream closure scheme. Therefore, the upstream connection scheme is preferred when a deep waterstop of transverse joint is laid.