Micro-CT is one of the best modalities in assessing bone morphology and microarchitecture in small animal models. Voxel size is directly related to the image resolution as it influences the bone morphology results. The purpose of this study was to assess the effects of t different thicknesses of structures on the trabecular bone qualitative parameters. It was also to find out the most appropriate voxel size when scanning a certain or specific body part with different thicknesses. Five BALB-C breed mice carcasses were scanned using two different voxel sizes of 18 and 35 µm. The scanning acquisition times were recorded to be compared and the trabecular bone parameters measurements were taken. Both trabecular number and trabecular separation were increased in thicker structures meanwhile bone volume fraction and trabecular thickness values were inconsistent with the increment of the structure thickness. The bone volume fraction, trabecular thickness and trabecular separation were higher in larger voxel size and vice versa for trabecular number. The scanning acquisition time has no apparent correlation with the trabecular bone parameters. The thickness of the bone structure did affect trabecular number and trabecular separation significantly but less affecting bone volume fraction and trabecular thickness. All trabecular bone parameters were found affected by the size of scanning voxel size used. The usage of 35 µm voxel was more recommended than 18 µm to save time and give out less radiation dose to specimen unless the detailed features of the trabecular pattern was very important.