Microsphere Sn3O4 flower-like structure has been successfully synthesized using a novel microwave-assisted hydrothermal method and comprehensively characterized by X-ray diffraction (XRD), field emission gun scanning electron microscope (FEG-SEM) and UV Vis spectrophotometer equipped with diffuse reflectance spectroscopy (UV-Vis DRS). In order to examine its photocatalytic performance, two synthetic azo-based dyes, acid yellow 17 (AY17) and direct blue 71 (DB71), have been used as organic pollutant models degraded under visible-light illumination. The results show that the negative charges of Sn3O4 produce higher efficiency photocatalytic activity on DB71 degradation compared to that on AY17 degradation. Further investigation has confirmed that the adsorption capacities played the main role in determining photocatalytic performance and differentiated the quantum yield of dye degradation. Moreover, the different adsorption capacities are generated by the formation of electrostatic interaction and repulsion between surface charge of Sn3O4 and dyes functional groups.