Abstract: The multi-trough aqueduct is a new type of aqueduct structure, which has the advantages of large cross section water flow, good overall workability and small deflection deformation of the channel body, but the channel body is more sensitive to uneven vertical deformation. In view of the fact that this type of structure is still the first in the water conservancy industry in our country, how to establish a multitrough aqueduct operation safety early warning monitoring index is an important problem in project operation management. At present, domestic scholars have put forward a number of monitoring models about aqueducts, but these models do not give clear monitoring indicators, and do not reflect the modern monitoring concept of “hierarchical monitoring, step-by-step warning”. Therefore, based on the previous research work, this paper proposes taking the non-uniform vertical deformation at the support as the main monitoring index, and the measured value of the reinforcement at the inner wall of the trough as the secondary monitoring index, and the research results can provide a reference for the safe operation of the multi-trough aqueduct.