Aqueduct, one kind of bridge structure overpassing a long space, is a significant structure for water delivery for the purpose of agricultural or domestic usage. Aqueduct has quite different loads from other forms of bridges, of which temperature effects due to the environment temperature change, such as seasonal weather or radiation from sunshine, are of great importance. With water flowing inside, the temperature boundary of aqueducts, especially for steel aqueducts, is much more complicated, and relevant researches are limited. In this paper, a 3D Finite Element Method (FEM) simulation process is presented to analyze temperature distribution on the cross-section of a new-type steel truss aqueduct, which belongs to the Water Transfer Project from Yangtze River to Huai River in China. ASHRAE clear-sky model is used to calculate the solar-radiation variation, including direct radiation, diffuse sky radiation, and ground reflected radiation on steel surfaces. The time-dependent sunshine radiation angle of incidence and shielding effect of steel trusses are considered. The water inside the aqueduct is also included in this model, which significantly influences the temperatures of the inner surfaces of the aqueduct. Several temperature distributions under critical conditions of winter and summer are shown in this study, and results of the empty aqueduct under the same circumstances are also provided as a comparison. The effects of wind speed, geographic latitude, and direction of the aqueduct are examined. The conclusions and approach provided by this study could serve as significant references for thermal design and control of similar steel truss aqueducts.