The invention discloses a machine tool motion compensation system based on temperature value analysis, and the system comprises a model building module which is used for building a time difference deformation model; an information collection module which is used for collecting the temperature of a machine tool target moving shaft, and recording the time t1 when the target moving shaft reaches first temperature and the time t2 when the target moving shaft reaches second temperature; and an error compensation module which is used for calculating the time difference t and the current deformation L, and carrying out the error compensation of the target moving shaft according to the current deformation L and an error allowed range. The system analyzes the temperature change conditions of the machine tool moving shaft through the time of the machine tool moving shaft in temperature rising, and determines the deformation according to the temperature change conditions of the machine tool moving shaft, and then makes an error compensation strategy for the machine tool moving shaft according to the actual deformation. The system gives consideration to three factors: temperature change, deformation and compensation, and achieves the step-by-step improvement. The system improves the effectiveness of the error compensation on the basis that the precision of a temperature change analysis result is guaranteed, and guarantees the machining precision of a machine tool.