Attention-based transformers have played an important role in wireless sensor network (WSN) timing anomaly detection due to their ability to capture long-term dependencies. However, there are several issues that must be addressed, such as the fact that their ability to capture long-term dependencies is not completely reliable, their computational complexity levels are high, and the spatiotemporal features of WSN timing data are not sufficiently extracted for detecting the correlation anomalies of multinode WSN timing data. To address these limitations, this paper proposes a WSN anomaly detection method that integrates frequency-domain features with dynamic graph neural networks (GNN) under a designed self-encoder reconstruction framework. First, the discrete wavelet transform effectively decomposes trend and seasonal components of time series to solve the poor long-term reliability of transformers. Second, a frequency-domain attention mechanism is designed to make full use of the difference between the amplitude distributions of normal data and anomalous data in this domain. Finally, a multimodal fusion-based dynamic graph convolutional network (MFDGCN) is designed by combining an attention mechanism and a graph convolutional network (GCN) to adaptively extract spatial correlation features. A series of experiments conducted on public datasets and their results demonstrate that the anomaly detection method designed in this paper exhibits superior precision and recall than the existing methods do, with an F1 score of 93.5%, representing an improvement of 2.9% over that of the existing models.