High-speed trains exert periodic dynamic loads on railway bridges. When the load excitation frequency aligns with a bridge's natural frequency, resonance occurs, leading to amplified vibrations. These vibrations critically threaten structural safety, diminish passenger comfort, and destabilize the ballast layer. This study introduces a mitigation strategy centered on optimizing bridge span lengths to suppress resonance in high-speed rail (HSR) bridge systems. We propose a novel analysis tool—the modal wave amplitude spectrum—to guide engineers in selecting the most effective span. This spectrum is derived in the spatial wavenumber domain from the residual free vibration of a beam after the moving train load has passed. The spectrum uniquely identifies two critical span conditions: (1) The optimal span for vibration cancellation corresponds to the trough (minimum value) of the wavenumber ratio. (2) The critical resonance span corresponds to the peak (maximum value) of the wavenumber ratio. Using this spectral method, we analyze the dynamic characteristics of HSR bridges. Our findings identify spans suitable for effective vibration reduction, illuminate potential sub-resonance issues, and propose appropriate vibration mitigation measures.