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This invention provides a method for modeling a cylinder motion system based on a physical information neural network, comprising: acquiring time-series data of the cylinder motion system, including time-series control quantities and system state quantities; constructing a physical information neural network model with a dynamic feature input layer and a physical parameter input layer, receiving the time-series control quantities and physical parameter vectors respectively; performing a nonlinear transformation on the physical parameter vectors through a physical parameter encoding network to obtain encoded physical feature vectors; fusing the time-series control quantities and physical feature vectors to form a joint input vector; inputting the joint input vector into the backbone neural network, synchronously predicting the system state quantities through multi-layer nonlinear transformations; constructing a composite loss function including a data loss term and a physical loss term; training the model using time-series data, updating the model parameters by minimizing the composite loss function until the model converges, thereby achieving high-precision modeling using only single motion data.