Ground-based microwave interferometry has been used extensively for dynamic deflection measurements of bridges. The Imaging by Interferometric Survey of Structures (IBIS-S) instrument is a system based on ground-based microwave interferometry, which consists of radar sensors for transmitting and receiving microwave and corresponding auxiliary units. To suppress the noise of the dynamic deflection of urban bridges obtained by ground-based microwave interferometry, by integrating singular value decomposition (SVD) and extreme-point symmetric mode decomposition (ESMD), a novel ESMD-SVD denoising method is proposed in this paper. First, the original bridge signal obtained by the IBIS-S sensor was decomposed to obtain a series of intrinsic mode functions (IMFs) and a signal trend term by ESMD. Second, the signal trend term was extracted and the IMFs were reconstructed, which removed the effect of the signal trend term on the singular value selection in SVD. SVD was used to eliminate the random noises and other noises in the reconstructed signal. Finally, the denoised signal obtained by SVD was superimposed on the trend term to obtain the final denoised signal. The results of both simulated and on-site experiments showed that the proposed ESMD-SVD method had a powerful signal denoising ability.