Safflomin A and betanin are incorporated into gelatin-chitooligosaccharide based complexes for stabilizing functional internal phase emulsions (HIPEs), which hold promise in 3D printing. Intermolecular interactions and good compatibility among gelatin, chitooligosaccharide and proper-content bioactive materials promoted the thermal stability (increased from 310.82 to 316.32 °C, or from 284.97 to 311.70 °C), dispersion stability (high UV absorbance) and microgel particles (around 358.67 or 408.30 nm) of complexes. The complexes illustrated great oil-water interfacial adsorption behaviors (kdiff = 0.29 mN m−1 s−0.5, π1600 = 21.71 mN/m) and dilatational viscoelasticity for interfacial membrane, implying high elasticity and interface stability. The strong droplet membrane and the compact gel network resulted in HIPEs to possess certain chemical stability (low color fading, e. g., under pH = 4), high centrifugation stability, shaking stability and freeze-thaw stability with low-diameter droplets. In addition to the excellent shear-thinning property (n1 < 1), HIPEs containing safflomin A or betanin had the systems with high degree of structuring (high η0 1.02 × 106 mPa s and 1.12 × 106 mPa s, respectively), excellent structure reversibility (high thixotropic index 7.62 and recovery index 71.76%; thixotropic index 6.87 and recovery index 77.29%, respectively), outstanding thixotropic performance (high thixotropic area 1872.01 Pa/s and 975.61 Pa/s, respectively), favorable self-supporting ability (recovery rates 92.01% and 94.61%, respectively), and high mechanical strength (yield stresses 21.32 Pa and 17.8 Pa after storage of 9 months), indicating the satisfactory structure maintainability. The screw-3D printing of HIPEs displayed high shape retention with low shape deviation (<5% for safflomin A- and betanin-based HIPEs), and certified the excellent printability. This study provides information for fabricating bioactive materials-HIPEs with desired structure, and manifests the potential of HIPEs in manufacturing functional, innovative food with high quality.