Aiming at the problem of inaccurate and time-consuming of the fault diagnosis method for large-scale ship engine, an intelligent diagnosis method for large-scale ship engine fault in non-deterministic environment based on neural network is proposed. First, the possible fault of the engine was analyzed, and the downtime fault of large-scale ship engine and the main fault mode were identified. On this basis, the fault diagnosis model for large-scale ship engine based on neural network is established, and the intelligent diagnosis of engine fault is completed. The experiment proved that the proposed method has high diagnostic accuracy, engine fault diagnosis takes only about 3s, with a higher use value.