Polyimide (PI)-based aerogels have been widely applied to aviation, automobiles, and thermal insulation because of their high porosity, low density, and excellent thermal insulating ability. However, the fabrication of PI aerogels is still restricted to the traditional molding process, and it is often challenging to prepare high-performance PI aerogels with complex 3D structures. Interestingly, renewable nanomaterials such as cellulose nanocrystals (CNCs) may provide a unique approach for 3D printing, mechanical reinforcement, and shape fidelity of the PI aerogels. Herein, we proposed a facile water-based 3D printable ink with sustainable nanofillers, cellulose nanocrystals (CNCs). Polyamic acid was first mixed with triethylamine to form an aqueous solution of polyamic acid ammonium salts (PAAS). CNCs were then dispersed in the aqueous PAAS solution to form a reversible physical network for direct ink writing (DIW). Further freeze-drying and thermal imidization produced porous PI/CNC composite aerogels with increased mechanical strength. The concentration of CNCs needed for DIW was reduced in the presence of PAAS, potentially because of the depletion effect of the polymer solution. Further analysis suggested that the physical network of CNCs lowered the shrinkage of aerogels during preparation and improved the shape-fidelity of the PI/CNC composite aerogels. In addition, the composite aerogels retained low thermal conductivity and may be used as heat management materials. Overall, our approach successfully utilized CNCs as rheological modifiers and reinforcement to 3D print strong PI/CNC composite aerogels for advanced thermal regulation.