The invention discloses a method and system for estimating the rotating speed of an engine. The method comprises the following steps that the engine exhaust pressure difference data at the current moment are continuously acquired and are subjected to multi-point moving average smooth filtering treatment, and the engine exhaust pressure difference value at this moment is obtained; a multi-point moving averaging method is adopted for calculating the engine exhaust pressure difference waveform average value; the difference value between the current engine exhaust pressure difference value and theengine exhaust pressure difference waveform average value is calculated, and the maximum value of the difference value is taken as the engine exhaust pressure difference waveform amplitude; the engine exhaust pressure difference waveform period is calculated through the engine exhaust pressure difference waveform amplitude, the engine exhaust pressure difference waveform average value and the engine exhaust pressure difference value; and the rotating speed of the engine is calculated through the engine exhaust pressure difference waveform period.