Liquid-crystalline (LC) bio-inspired materials based on colloidal nanoparticles with anisotropic morphologies such as sheets, plates, rods and fibers were used as functional materials. They show stimuli-responsive behaviour under mechanical force and in electric and magnetic fields. Understanding the effects of external stimuli on the structures of anisotropic colloidal particles is important for the development of highly ordered structures. Recently, we have developed stimuli-responsive hydroxyapatite (HAP)-based colloidal LC nanorods that are environmentally-friendly functional materials. In the present study, the ordering behaviour of HAP nanorod dispersions, which show LC states, has been examined using in situ small-angle neutron scattering and rheological measurements (Rheo-SANS) under shearing force. The structural analyses and dynamic viscosity observations provided detailed information about the effects of shear force on the structural changes of HAP nanorods in D2O dispersion. The present Rheo-SANS measurements unraveled three kinds of main effects of the shear force: the enhancement of interactions between the HAP nanorods, the alignment of HAP nanorods to the shear flow direction, and the formation and disruption of HAP nanorod assemblies. Simultaneous analyses of dynamic viscosity and structural changes revealed that the HAP nanorod dispersions exhibited distinctive rheological properties accompanied by their ordered structural changes.