To address the noise issue in the measured vibration signals of spillway radial gate discharge, this paper utilizes the Multiverse Optimization Algorithm (MVO) to optimize the number of decomposition modes (K) and the penalty factor (α) in Variational Mode Decomposition (VMD). This approach ensures improved efficiency of VMD decomposition while maintaining accuracy. Subsequently, the obtained Intrinsic Mode Functions (IMFs) from VMD decomposition are classified based on Multi-scale Permutation Entropy (MPE). IMFs are divided into pure components and noisy components; the noisy components are processed with Wavelet Threshold Denoising (WTD), while the pure components are overlaid and reconstructed to obtain the denoised vibration signal of the gate. Comprehensive comparisons involving artificial signal simulations, gate flow-induced vibration model tests, and numerical simulations lead to the following conclusions: compared to other algorithms, the proposed combined denoising method (MVO-VMD-MPE-WTD) achieves the highest signal-to-noise ratio (SNR) in both the frequency and time domains for artificial signals, while yielding the lowest mean square error (MSE). In the gate flow-induced vibration model tests, the method significantly reduces noise in the vibration signals and effectively preserves characteristic information. The error in preserving characteristic information across model tests and numerical simulations is kept below 1%. Furthermore, compared to other optimization algorithms, the MVO demonstrates higher computational efficiency. The parameter-optimized combined denoising method proposed in this study provides insights into denoising measured vibration signals of hydraulic spillway radial gates and other drainage structures, and it opens possibilities for exploring more efficient optimization algorithms for achieving online monitoring in the future.