To achieve high-precision geomagnetic matching navigation, a reliable geomagnetic anomaly basemap is essential. However, the accuracy of the geomagnetic anomaly basemap is often compromised by noise data that are inherent in the process of data acquisition and integration of multiple data sources. In order to address this challenge, a denoising approach utilizing an improved multiscale wavelet transform is proposed. The denoising process involves the iterative multiscale wavelet transform, which leverages the structural characteristics of the geomagnetic anomaly basemap to extract statistical information on model residuals. This information serves as the a priori knowledge for determining the Bayes estimation threshold necessary for obtaining an optimal wavelet threshold. Additionally, the entropy method is employed to integrate three commonly used evaluation indexes—the signal-to-noise ratio, root mean square (RMS), and smoothing degree. A fusion model of soft and hard threshold functions is devised to mitigate the inherent drawbacks of a single threshold function. During denoising, the Elastic Net regular term is introduced to enhance the accuracy and stability of the denoising results. To validate the proposed method, denoising experiments are conducted using simulation data from a sphere magnetic anomaly model and measured data from a Pacific Ocean sea area. The denoising performance of the proposed method is compared with Gaussian filter, mean filter, and soft and hard threshold wavelet transform algorithms. The experimental results, both for the simulated and measured data, demonstrate that the proposed method excels in denoising effectiveness; maintaining high accuracy; preserving image details while effectively removing noise; and optimizing the signal-to-noise ratio, structural similarity, root mean square error, and smoothing degree of the denoised image.