Aiming at the aging problem of the Nangudong masonry aqueduct in the Hongqi Canal, a three-dimensional finite element mesh was generated based on the Hypermesh software, and a three-dimensional finite element model for the aqueduct was established. The ABAQUS software was used to calculate the structural stress and deformation of the aqueduct. The structure stability of the aqueduct was checked by the material mechanics method. The results show that the maximum settlement of the pier foundation is 3. 05 mm. The maximum settlement difference of adjacent pier foundation is 0. 43 mm. The maximum compressive stress of the aqueduct is 4. 56 MPa and the maximum tensile stress is 1. 93 MPa, which appear in the local area at the side wall of the aqueduct. The minimum safety coefficients of anti-sliding stability and anti-capsizing stability of the groove pier are 10. 1 and 2. 4, respectively, both larger than the allowable values. Comprehensive analysis shows that the aqueduct is safe.