Abstract3D pose transfer over unorganized point clouds is a challenging generation task, which transfers a source’s pose to a target shape and keeps the target’s identity. Recent deep models have learned deformations and used the target’s identity as a style to modulate the combined features of two shapes or the aligned vertices of the source shape. However, all operations in these models are point-wise and independent and ignore the geometric information on the surface and structure of the input shapes. This disadvantage severely limits the generation and generalization capabilities. In this study, we propose a geometry-aware method based on a novel transformer autoencoder to solve this problem. An efficient self-attention mechanism, that is, cross-covariance attention, was utilized across our framework to perceive the correlations between points at different distances. Specifically, the transformer encoder extracts the target shape’s local geometry details for identity attributes and the source shape’s global geometry structure for pose information. Our transformer decoder efficiently learns deformations and recovers identity properties by fusing and decoding the extracted features in a geometry attentional manner, which does not require corresponding information or modulation steps. The experiments demonstrated that the geometry-aware method achieved state-of-the-art performance in a 3D pose transfer task. The implementation code and data are available at https://github.com/SEULSH/Geometry-Aware-3D-Pose-Transfer-Using-Transformer-Autoencoder.