In order to diagnose the abnormal noise of a certain type of diesel generating set, a new method of empirical mode decomposition (EMD) and Hilbert transform is proposed to analyze the non-stationary vibration signals of the generator main bearing, which can effectively extract the time-frequency characteristics of main bearing vibration signals. Comprehensive analyses are made based on the signals of diesel generating set noise, generator main bearing vibration and shaft system torsional vibration. The diagnostic results show that the torsional vibration amplitude values of the shaft system are too high, with diesel engine excitation causing the relative motion of pin coupling rubber parts surfaces. This procedure can produce dry friction force, which leads to the intermittent abnormal vibration noise of the shaft system. This method has reference value for the abnormal vibration noise diagnosis caused by friction of the rotary shaft system components.