Photodecomposition of pentacene films grown on the atomically controlled SrTiO3(001) (STO) surfaces was investigated by atomic force microscopy. The photodecomposition was found to occur only when the coverage of the pentacene film was less than 1 ML on the TiO2-terminated STO(001). When the oxygen adsorption is a rate-limiting step, the decomposition rate is nearly proportional to the surface area uncovered with pentacene island, while at the last stage of the decomposition it is in proportion not to the coverage of the pentacene islands but to the perimeter of the pentacene islands. The SrO-terminated STO(001) surface exhibits very little activity in the photodecomposition of the pentacene. The exponential decay of the rate constant with the SrO coverage suggests that it is attributed to some chemical effect such as the formation of Sr hydroxide at the SrO-terminated surface.