Formulating a multi-scan method applied to an X-ray microscope CT with synchrotron radiation, we attempted to analyze the 3D functional structure of osteocyte canaliculi inside the cortical bone of a mouse tibia. We employed a two-method combination to scan the same position of the specimen. To extract the internal bone canalicular structure, we first combined a Talbot interferometer with an X-ray microscope, and applied a differential phase imaging method to measure the absolute value of bone mineral around the canaliculi. Next, we used the X-ray microscope without the Talbot interferometer under a defocus condition, moving the specimen toward the zone plate by 6 mm. This defocus contrast method visualizes the canaliculi by emphasizing the edges of the bone. We performed CT scans by the two configurations and precisely aligned resultant 3D images so that the same position in the specimen is compared. We could extract the osteocyte canaliculi and evaluate the mineral density of their surroundings. The degree of mineralization varied for each osteocyte lacuna and canaliculus. The multi-scan microscopic X-ray CT is a powerful tool for analyzing bone mineralization.