The concrete bridge is likely to produce fatigue cracks during long period of service due to the moving vehicular loads and the degeneration of materials. This paper deals with the time-frequency analysis of a coupled bridge-vehicle system. The bridge is modeled as an Euler beam with breathing cracks. The vehicle is represented by a two-axle vehicle model. The equation of motion of the coupled bridge-vehicle system is established using the finite element method, and the Newmark direct integration method is adopted to calculate the dynamic responses of the system. The effect of breathing cracks on the dynamic responses of the bridge is investigated. The time-frequency characteristics of the responses are analyzed using both the Hilbert-Huang transform and wavelet transform. The results of time-frequency analysis indicate that complicated non-linear and non-stationary features will appear due to the breathing effect of the cracks.