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This paper presents vibration-based damage detection (VBDD) for testing a steel-concrete composite bridge deck in a laboratory using both model-based and non-model-based methods. Damage that appears on a composite bridge deck may occur either in the service condition or in the loading condition. To verify the efficiency of the dynamic test methods for assessing different damage scenarios, two defect cases were designed in the service condition by removing the connection bolts along half of a steel girder and replacing the boundary conditions, while three damage cases were introduced in the loading condition by increasing the applied load. A static test and a multiple reference impact test (MRIT) were conducted in each case to obtain the corresponding deflection and modal data. For the non-model-based method, modal flexibility and modal flexibility displacement (MFD) were used to detect the location and extent of the damage. The test results showed that the appearance and location of the damage in defect cases and loading conditions can be successfully identified by the MFD values. A finite element (FE) model was rationally selected to represent the dynamic characteristics of the physical model, while four highly sensitive physical parameters were rationally selected using sensitivity analysis. The model updating technique was used to assess the condition of the whole deck in the service condition, including the boundary conditions, connectors, and slab. Using damage functions, Strand7 software was used to conduct FE analysis coupled with the MATLAB application programming interface to update multiple physical parameters. Of the three different FE models used to simulate the behavior of the composite slab, the calculated MFD of the shell-solid FE model was almost identical to the test results, indicating that the performance of the tested composite structure could be accurately predicted by this type of FE model.