Abstract: The combined unit (MU), as the core equipment of the process layer in an intelligent substation, its sampling value synchronization accuracy directly determines the working reliability of secondary equipment such as relay protection and electric energy metering. Aiming at the problems of inconsistent channel delays and difficulty in suppressing dynamic residuals during the synchronization of sampling values of merged units, this paper proposes a joint compensation method of reference alignment and second-order Lagrangian interpolation. Channel alignment is achieved by eliminating static delays through FIFO, and then a second-order interpolation model is constructed to compensate for dynamic residuals in real time, which is implemented in a pipeline in FPGA. Experiments show that the steady-state average error of this method is as low as 0.011%, and the maximum instantaneous error under transient conditions is only 0.041%, which is better than the engineering threshold of 0.05%. Moreover, the dynamic recovery time is shortened to 1.7ms, which can effectively improve the sampling synchronization accuracy and response speed under complex working conditions and meet the operation requirements of the power grid.