Silver decorated TiO2 nanotube arrays (TNTAs) show great potential applications for photocatalysis and gas sensors. In this work, we report an improved strategy to modify the morphology of flow-through TiO2 nanotube arrays (f-TNTAs) for homogeneous Ag nanoparticle loading, and their photocatalytic activities are also investigated. Firstly, TNTAs were fabricated by potentiostatic anodization in fluoride-containing electrolytes. Subsequently, a high voltage was immediately exerted, and then a low potential was applied at the end of anodization process. The as-prepared f-TNTAs with improved bottom morphologies were finally obtained. This new kind of support was immersed in AgNO3 solution, and then the absorbed silver ions were reduced to metallic Ag0 by UV light. Compared with conventional TiO2 nanotube arrays (c-TNTAs), the modified f-TNTAs show a better ability for the dispersion of Ag nanoparticles (Ag NPs) in different regions (upper, central and bottom region) of the nanotubes. A series of testing measures (XPS, EDX, SEM and XRD) were adopted to confirm this facile process. Ag decorated f-TNTAs were used as photocatalysts for the degradation of Methyl Orange (MO) under UV light. The degradation rate could reach 54 in 10 min, and the complete degradation of MO was observed after 30 min. These results were much better than that of Ag decorated c-TNTAs. The modified f-TNTAs via our method can also be used to couple with other noble metals or compound semiconductors. These composite structures are expected to find potential applications in photoelectric devices, gas sensors, and photocatalysis.