Flavonoid-metal complexes possess more effective functional properties than flavonoids. However, the research of iso-orientin (Iso)-metal complex has rarely been reported. In this study, Iso-zinc complex (Iso-Zn, [Zn3(C21H14O11)2]·4H2O) had been synthesized and characterized. From the UV-vis spectra and IR spectra, the 4-carbonyl group in the C-ring of Iso was involved in the metal chelation besides A-ring and B-ring hydroxyl group. Thermal gravimetric analysis and the water contact angle test showed that Iso-Zn had higher thermal stability and better hydrophilicity than Iso, respectively. The radical scavenger and antibacterial potencies of Iso-Zn were significantly stronger than those of Iso. Furthermore, Iso-Zn showed lower erythrocytes hemolysis ratio and cytotoxicity. The present study demonstrated that Iso-Zn exhibited better water solubility, antioxidative and antibacterial activities, and lower cytotoxicity and provided a theoretical basis for expanding the utilization scope of Iso through enhancing its hydrophilicity.