Abstract: Wading projects are likely to bring about changes of the original hydrodynamic conditions of the river, and this may further affect the flood discharge capacity of the river course. Thus, it is of great significance to study the flood risk of the river course with or without the wading projects, so that we can well maintain the project, regulate river course and ensure regional flood control security. Based on the random simulation of four uncertain factors, namely peak flood discharge, initial water level, river course roughness and dike elevation, this paper analyzed the stress of aqueduct under flood action, and then calculated the water surface line of the river. Combined with theforce conditions and water surface line calculation results, the conventional Monte Carlo method and the Monte Carlo method based on Latin hypercube sampling were both used to calculate the flood risk of river course with or without an aqueduct. The results show that:（1） When the water level in Gangqian Aqueduct is 0.5, 1.0, 1.5 and 2.0 m, the flood discharge capacity of Qingfeng Mountain stream, compared with its designed discharge of 1 200 m~3/s, respectively decreases by 36.68%, 27.87%, 19.00% and 10.05%.（2） In the case of having no aqueduct in its river course, the flood risk of Qingfeng Mountain stream course is 0.007. In the case of having Gangqian Aqueduct in its river course, when the water level in the aqueduct was 0.5, 1.0, 1.5 and 2.0 m respectively, the flood risk of Qingfeng Mountain stream course is 0.34, 0.045, 0.016, 0.012 in turn.（3） Keep the water level in Gangqian Aqueduct at the highest value within the safe range. When the discharge of Qingfeng Mountain stream exceeds 1 600 m~3/s, the flood risk of its river course still rises significantly with the increase in the flood flow. Therefore, in this case, Gangqian Aqueduct would have to be scrapped to ensure the flood discharge capacity of Qingfeng Mountain stream.（4） Both the conventional Monte Carlo method and the Monte Carlo method based on Latin Hypercube Sampling are suitable for assessing the influence of aqueduct on flood risk of river course, and the latter has better convergence. In summary, building adueducts in river courses would have a negative impact on the river courses’ flood discharge capacity. It results in the flood discharge capacity of the river course being lower than the designed discharge, and further, led to the flood risk of river course increasing. To a certain extent, raising water level in the aqueduct can reduce the flood risk of river course.