Series of TiO2–ZnO heterojunction composite films with different n(Zn)/n(Ti) ratios were prepared by UDP450 magnetron sputter ion plating equipment, and the mole ratio of Zn to Ti was controlled by adjusting the current values of sputtering target. The effects of n(Zn)/n(Ti) on the microstructures of TiO2–ZnO films were investigated by SEM, AFM, Raman and XPS, and their photocatalytic decomposition of methyl orange solutions was evaluated. The results show that an increase in n(Zn)/n(Ti) typically results in a decrease in the grain size of composite films firstly and then an increase of grain size, while an increase in n(Zn)/n(Ti) leads to an increase in film roughness firstly and then a decrease in film roughness. Both grain size and roughness of TiO2–ZnO films reach the maximum and minimum at n(Zn)/n(Ti) of 1/9.3, respectively. The n(Zn)/n(Ti) shows little effect on the valences of Zn and Ti elements, which mainly exist in the form of TiO2 and ZnO phases. The n(Zn)/n(Ti) has influence on the amount of anatase/rutile TiO2 heterojunction in the film. With increase of the n(Zn)/n(Ti), the absorption intensity of the composite film increases and the absorption region extends to 450 nm, which is redshifted as much as 150 nm in comparison with the pure TiO2 films. However, the photocatalytic abilities of heterogeneous composite films do not depend on the n(Zn)/n(Ti) but rather on the microstructures of the TiO2–ZnO composite films. Degradation rate of the film reaches the maximum and the photocatalytic decomposition of pollutants works best when n(Zn)/n(Ti)=1:9.3.