The invention discloses a method and system for predicting the operating state of an engine. The method comprises the steps that according to the oil needle adjustment value of the engine and the altitude of the working environment, the nonlinear order and memory span of each influence factor are determined, and the influence factors comprise the air door opening degree, the atmospheric pressure and the atmospheric temperature; a nonlinear model of the engine is determined according to the nonlinear orders and the memory spans; the engine is stimulated, and sample data of the air door opening degree, the atmospheric pressure, the atmospheric temperature and the rotating speed of the engine are collected; and according to the sample data and the nonlinear model, a target model of the engine is determined and used for predicting the operating state of the engine. According to the method and system, for the nonlinear characteristic of the piston engine, the nonlinear model capable of accurately reflecting an actual system is adopted, the multi-input and single-output nonlinear target model with the air door opening degree, the atmospheric pressure and the atmospheric temperature serving as input and the rotating speed of the engine serving as output is built, and the operating state of the engine can be accurately predicted.