Photospheric bright points (PBPs) and chromospheric bright points (CBPs) reflect the cross sections of magnetic flux tubes at different heights of the lower solar atmosphere. We aim to study the fine 3D structures and transportation dynamics of the magnetic flux tubes using G-band and simultaneous Ca II H image-series from the Solar Optical Telescope (SOT) on board Hinode. A 3D track-while-detect method is proposed to detect and track PBPs and CBPs. The mean values of equivalent diameters, maximum intensity contrasts, transverse velocities, motion ranges, motion types, and diffusion indices of PBPs and CBPs are 180 +/- 20 and 210 +/- 30 km, 1.0 +/- 0.1 < IQS-G > and 1.2 +/- 0.1 < IQS-Ca >, 1.6 +/- 0.8 and 2.7 +/- 1.4 km s(-1), 1.5 +/- 0.6 and 1.7 +/- 0.8, 0.8 +/- 0.2 and 0.6 +/- 0.2, and 1.7 +/- 0.7 and 1.3 +/- 0.7, respectively. Moreover, the ratios of each CBP characteristics to its corresponding PBP are derived to explore the change rates of the flux tubes. The corresponding ratios are 1.2 +/- 0.2, 1.2 +/- 0.1, 1.9 +/- 0.1, 1.4 +/- 0.3, 0.7 +/- 0.2, and 0.9 +/- 0.4, respectively. The statistical results imply that the majority magnetic flux tubes expand slightly with increasing solar height, look brighter than their surroundings, show a higher transverse velocity, a wider motion range, and a more erratic path, but the majority of the flux tubes diffuse slightly slower. The phenomenon might be explained by the conservation of momentum combined with a decrease in density. The more erratic path leads to a swing or twist of the flux tubes and therefore guides magnetohydrodynamic waves.