To effectively suppress the geyser in the storage tunnel system, the suppression effects of two different shaft forms on the geyser are investigated based on the 3-D numerical simulation. The results show that the protruding shaft can induce the separation of the gas-column head, and decrease the local pressure and the kinetic energy of the upper water, resulting in the suppression on the geyser. The shunt shaft can make one bin to undertake the other bin of the upward water, prevent most of the water moving up, and increase the leaky velocity of the upper water, resulting in the suppression on the geyser. The protruding shaft has better suppression effect on the geyser, and the geyser intensity can be reduced by 60%.