Transparent, well-aligned TiO2 nanotube arrays (NTAs) with controllable dimensions are grown on glass substrates via atomic layer deposition (ALD) of TiO2 onto free-standing porous anodic alumina (PAA) templates. Photodegradation of aqueous methylene blue (MB) solution and solid stearic acid (SA) film using TiO2 NTAs of various wall thicknesses are investigated. The Pd functionalized TiO2 NTAs, with a wall thickness of 15 nm and height of 200 nm, has the highest photodegradation efficiency at 76% after 4 h of UV irradiation. These functionalized NTAs are able to photodegrade MB molecules completely as no obvious demethylated byproducts are observed during the process. It also demonstrates excellent photocatalytic activity for solid contaminants such as SA film. By using the ALD technique, the nanotube wall thickness can be precisely controlled so that it is sufficiently thin to be transparent while sufficiently thick for excellent photocatalytic performances. The transparent TiO2 NTAs on glass substrates with excellent photocatalytic properties might have potential applications in self-cleaning coating, transparent electronics, and solar cells.