Online training framework based on discriminative correlation filters for visual tracking has recently shown significant improvement in both accuracy and speed. However, correlation filter-base discriminative approaches have a common problem of tracking performance degradation when the local structure of a target is distorted by the boundary effect problem. The shape distortion of the target is mainly caused by the circulant structure in the Fourier domain processing, and it makes the correlation filter learn distorted training samples. In this paper, we present a structure–attention network to preserve the target structure from the structure distortion caused by the boundary effect. More specifically, we adopt a variational auto-encoder as a structure–attention network to make various and representative target structures. We also proposed two denoising criteria using a novel reconstruction loss for variational auto-encoding framework to capture more robust structures even under the boundary condition. Through the proposed structure–attention framework, discriminative correlation filters can learn robust structure information of targets during online training with an enhanced discriminating performance and adaptability. Experimental results on major visual tracking benchmark datasets show that the proposed method produces a better or comparable performance compared with the state-of-the-art tracking methods with a real-time processing speed of more than 80 frames per second.