Federated learning can achieve multi-party data-collaborative applications while safeguarding personal privacy. However, the process often leads to a decline in the quality of sample data due to a substantial amount of missing encrypted aligned data, and there is a lack of research on how to improve the model learning effect by increasing the number of samples of encrypted aligned data in federated learning. Therefore, this paper integrates the functional characteristics of deep learning models and proposes a Variational AutoEncoder Gaussian Mixture Model Clustering Vertical Federated Learning Model (VAEGMMC-VFL), which leverages the feature extraction capability of the autoencoder and the clustering and pattern discovery capabilities of Gaussian mixture clustering on diverse datasets to further explore a large number of potentially usable samples. Firstly, the Variational AutoEncoder is used to achieve dimensionality reduction and sample feature reconstruction of high-dimensional data samples. Subsequently, Gaussian mixture clustering is further employed to partition the dataset into multiple potential Gaussian-distributed clusters and filter the sample data using thresholding. Additionally, the paper introduces a labeled sample attribute value finding algorithm to fill in attribute values for encrypted unaligned samples that meet the requirements, allowing for the full recovery of encrypted unaligned data. In the experimental section, the paper selects four sets of datasets from different industries and compares the proposed method with three federated learning clustering methods in terms of clustering loss, reconstruction loss, and other metrics. Tests on precision, accuracy, recall, ROC curve, and F1-score indicate that the proposed method outperforms similar approaches.