This study proposes an input decoupling analysis method based on the pulse test and the traditional operational transfer path analysis (OTPA) method for the OTPA transmission path analysis when the input is strongly coupled, and the algorithm is verified for analysis optimization of results. An experimental model of the dual excitation source is established in the laboratory. Experimental comparison studies show that the OTPA method, which is based on signal decoupling, inhibits the influence of cross-coupling among the source signals during OTPA analysis and effectively improves the accuracy of the transmission path test and analysis. The OTPA method is applied to analyze the transfer path of the vibration and noise of the carriages of the electric multiple unit (EMU) train (a high-speed train in China). The false peak frequency in the traditional OTPA method is eliminated, and the accuracy of the analysis is improved.