This paper presents a method for identifying fraudulent fund transfers using real bank data, analyzing customer information, transactional activities, and customer relationships. The preprocessing step transforms high-dimensional, irregular transaction time series into regular time series, then further compresses them in a latent space using a self-attention-based autoencoder. To address the scarcity of fraudulent data samples and mitigate training issues caused by data imbalance, various deep generative models, including the conditional variational autoencoder and Wasserstein generative adversarial network, are applied to generate additional fraudulent raw data and augment fraud samples in latent space. The reparameterization trick is integrated into the encoder–decoder structure to boost the model’s generative capabilities. Additionally, a Graph Neural Network (GNN) is used to model customer relationships. The proposed approach utilizes end-to-end learning, integrating the autoencoder’s reconstruction loss, KL divergence loss (when reparameterization trick is applied), and classification loss for fraud detection. To optimize computational resources, neighborhood sampling for GNN is combined with mini-batch training for the autoencoder, improving both training efficiency and model reliability. Comprehensive experiments demonstrate the effectiveness of the proposed fusion network, highlighting the importance of each component and preprocessing step. For example, the areas under the precision–recall curves for fraud detection show notable improvements in our model. For suspicious transactions identified by the bank’s rules, other models range from 0.66% to 22.15%, while our model reached 27%. For non-suspicious transactions, other models range from 2.53% to 22.00%, with our model achieving 22.90%. This model has potential for wider applications in anomaly detection, particularly in datasets with irregular time series and complex customer relationships.