Dimension reduction (DR) is commonly utilized to capture intrinsic structure and transform high-dimensional data into low-dimensional space while retaining meaningful properties of original data. It is used in a wide variety of applications such as image recognition, single-cell sequencing analysis, and biomarker discovery. However, contemporary parametric-free and parametric DR techniques suffer from several major shortcomings, such as the inability to preserve both global and local features and the pool generalization performance. On the other hand, regarding explainability, it is crucial to comprehend the embedding process, especially the contribution of each feature to the embedding process while understanding how each feature affects the embedding results that identify critical components and helps diagnose the embedding process. To address these problems, we have developed a deep neural network method called EVNet which provides not only excellent performance in structural maintainability but also explainability to the DR therein. EVNet starts from data augmentation and with a manifold-based loss function to improve embedding performance. The explanation is based on saliency maps and is aimed to examine the trained EVNet parameters and contributions of components during the embedding process. The proposed techniques are integrated with a visual interface to help the user to adjust EVNet to achieve better DR performance and explainability. The interactive visual interface makes it easier to illustrate the data features, compare different DR techniques, and investigate the explainability of DR. An in-depth experimental comparison is provided which shows that EVNet consistently outperforms the state-of-the-art methods in both performance measures and explainability.