Advanced composite aerogel materials have attracted much attention due to the unique structure and properties. However, the efficient manufacturing process and structural stability were still a challenge. Herein, a novel hydroxyapatite nanowires/polyimide (HAnws/PI) composite aerogel was synthesized by the ultralong HAnws combined with polyamic acid via directional freezing and thermal imidization. Among them, the HAnws and PI intertwined to form a three-dimensional network structure, which decreased the volume shrinkage of aerogel in thermal imidization from 42.9% to 12.6%, resulting in high porosity (>96%) and low density (0.0329–0.0431 g cm−3). In addition, the HAnws/PI aerogel with layered porous structure exhibits obvious anisotropic mechanical properties. The axial specific modulus as high as 78.05 kN m kg−1 and radial high elasticity can withstand 100 cycles of fatigue resistance. Moreover, the lowest radial thermal conductivity at 32.21 mW m−1 K−1 and the maximum of the anisotropy factor was 2.2, which was very suitable for insulation pipes to prevent additional heat loss. Therefore, the novel nanofibers reinforced organic aerogel was expected to provide more abundant functional applications in energy efficiency.