Gardenia blue could be effectively stabilized by gelatin and could be further enhanced by high-temperature based covalent-crosslinking reaction. The crosslinking reaction between amino acids and genipin promotes the generation of new gardenia blue molecules, facilitates the stable network structure, and improves the thermal stability of gelatin-gardenia blue systems (T₁ increased to 90 °C and T₂ increased from 310 °C to 315 °C), which is confirmed by UV absorbance, amino acid analysis, TGA, FTIR, XRD, SEM and particle size (774 nm). The treated samples also possess high resistance against acid and alkali chemicals (A/A0 ≈ 1) because of hyperchromic effect, high resistance against UV irradiation (ΔE < 5) due to the compact nanosized matrix, as well as great shear-thinning behavior (n < 1) and thixotropy (96.83%). Its applications in 2D writing/printing, food functionalization and 3D printing on paper and various food, illustrate high-definition patterns and satisfying colors. Overall, the crosslinked gelatin-gardenia blue based system has potential application in food under high-temperature, acidic, basic or salty conditions, with wide consumption groups and high food industry values.