Temperature changes have a great impact on guided wave propagation, but the composite error caused by temperature and other factors on guided waves is rarely studied, and pipelines are often in various severe environments. It is necessary to study the composite error between temperature changes and different working conditions. Regarding the relationship between the water-filled pipeline and the temperature change, a new compensation idea is proposed, that is, the signal set is used to match the similar baseline signal, and the water filling information is judged at the same time, then the time domain part of the monitoring signal is stretched by the baseline stretching method, and finally the corresponding maximum residual amplitude and the water-filling deviation are subtracted to complete the composite error compensation of the signal. The feasibility of the method was analyzed by COMSOL simulation, and experiments were designed to verify the effect. The experimental results show that the average amplitude of the residual signal after compensation is 5 dB lower than the average amplitude of the residual signal after compensation, that is, the method can effectively compensate for the composite error caused by temperature change and water filling.