The invention relates to a working balance fault diagnosis method and device for a diesel engine based on the instantaneous rotating speed. A signal synchronization technology is used to obtain the top dead center (TDC) and crankshaft corner signals of the diesel engine, the TDC signal serves as an identification to identity a complete work cycle of the diesel engine, the crankshaft corner signal is used to obtain the instantaneous rotating speed of each tooth of a fluted disc of the diesel engine, tooth average, period average and filtering technology are used to process the obtained instantaneous rotating speed signals and further to obtain a fluctuation diagram as well as the fluctuation ratio of the instantaneous rotating speed, a maximal working peak value corresponding to each cylinder is extracted according the practical TDC position and ignition sequence of the diesel engine, the maximal working peak values of the corresponding cylinder in multiple complete working periods in the same working condition of the diesel engine are compared and analyzed, and when deviation is over 30%, it is determined that the marine diesel engine has a fault that that gaps of an inlet valve is too large.