Cross building is inevitable in water diversion projects, and the structural state of cross buildings is crucial to the safe operation of the project. Based on a water transfer project in Henan Province, a three-dimensional finite element model of cross-crossing of water pipeline structures in the inverted siphon and water transfer project of the South-North Water Transfer Central Project was established by taking into account the coupling effect between soil-water-structure in the process of water transfer and diversion. The structural state effect of cross building under each simulation operating condition was analyzed by considering the periods of unconstructed structure, completion, normal operating. The results show that the cross-crossing building has impact on the existing building, especially for the large change of structural state in cross part. The maximum tensile stress in the inverted siphon structure increases from 0.54 MPa to 0.97 MPa, and the maximum settlement increases from -1.38 mm to -1.90 mm; The tensile stress in the aqueduct increases from 1.03 MPa to 1.34 MPa, and the maximum settlement increases from -3.78 mm to -4.07 mm. The stress value and settlement amount can meet the engineering requirements. Moreover, with the increase of the buried depth of the two supports of the water pipeline, the less the impact on inverted siphon is. The research results can provide reference for the analysis of similar projects.