The self-heating effect of a laboratory X-ray computed tomography (CT) scanner causes slight change in its imaging geometry, which induces translation and dilatation (i.e., artificial displacement and strain) in reconstructed volume images recorded at different times. To realize high-accuracy internal full-field deformation measurements using digital volume correlation (DVC), these artificial displacements and strains associated with unstable CT imaging must be eliminated. In this work, an effective and easily implemented reference sample compensation (RSC) method is proposed for in-situ systematic error correction in DVC. The proposed method utilizes a stationary reference sample, which is placed beside the test sample to record the artificial displacement fields caused by the self-heating effect of CT scanners. The detected displacement fields are then fitted by a parametric polynomial model, which is used to remove the unwanted artificial deformations in the test sample. Rescan tests of a stationary sample and real uniaxial compression tests performed on copper foam specimens demonstrate the accuracy, efficacy, and practicality of the presented RSC method.