Aiming at the problem of precision loss caused by errors in dynamic testing system, a dynamic error tracing method based on ensemble empirical mode decomposition and BP neural network was proposed. Based on the theory of the whole system dynamic precision, the method decomposed the total output error of the dynamic test system through the EEMD, and performed Hilbert transform on the single error obtained by the decomposition, analyzed the amplitude-frequency characteristics of the error signals, and then used BP neural network to fitting and tracing. The simulation results show that the method can trace back the error module in the dynamic test system effectively, and the accuracy of deviation is up to 10-2, compared with empirical mode decomposition, the method has better traceability effect and avoids mode aliasing problems existing in EMD, it is feasible and applicable.