In combination with the prestressed concrete structure design of inverted siphon down across the Nansha River of the Center Route Project of Water Transfer from South to North, the three dimensional finite element analysis method was used to study the effects of foundation changes on the behaviors of inverted siphon structure under several design conditions. The calculated results show that the regularity of foundation has more influence on the behaviors of inverted siphon under unevenness state, and that the marked improvement to the behaviors of inverted siphon can be obtained by displacing soil adjusting the regularity of foundation, especially to the behaviors of bottom slab of inverted siphon.