Objective To develop a novel measurement system composed of micro-CT, mechanical loading device and digital volume correlation (DVC) technique, so as to measure the three-dimensional microstructural deformation field in bone tissue. Methods Uniaxial compression was applied on the specimen with the micromechanical loading device, and CT scans were also conducted while maintaining the same loads; then sequential CT images were matched and searched accordingly by DVC method to calculate the micro-displacement in the specimen along three directions before and after loading; repeated scanning of zero-displacement and rigid body translation were used to evaluate the accuracy and precision of the system. The three-dimensional distribution of displacement field in bovine cancellous bone was measured by the system. Results The result from repeated scanning of zero-displacement showed that the highest accuracy of measurement was performed in the loading direction and the precision was less than tenth of the CT resolution. The result of rigid body translation showed that the standard deviation was 0.001~0.002 μm. For cancellous bone specimen under the load of 600 N, the range of micro-displacement was 100.35~110.25 μm, with multilayer field distribution. Conclusions The accuracy and precision of this measurement system can meet the requirement of DVC method. It is proved that this system can be used for measuring the three-dimensional micro-deformation field in the cancellous bone and as a measurement platform for investigating the relationship between deformation distribution and structural response in bone tissue for the future research.