Four kinds of Mo targets with different microstructures were sputtered by the same sputtering line under the same sputtering process. Microstructures (face and fractured cross-section) of sputtered films were analyzed with SEM, and the orientation of crystals and square resistance were measured with XRD and four-probe array method, respectively. Influence of Mo target’s microstructure on deposition rate and square resistance of the sputtered film were discussed. Results show that the sputtering film’s morphology of different Mo-targets is rarely different. When Mo targets are with 80% fine grains under 50 μm, the uniformity of sputtering film’s thickness and resistance are satisfied. The preferred orientation of Mo sputtered film is mostly (110). The target microstructures have little effect on sputtering film crystals’ orientation. When the Mo target’s grain size is finer and the area rate of grain boundary is higher, the sputtering film has faster deposition velocity and the sputtering film’s thickness is larger. The thickness reduction of sputtering target is more homogeneous, which raises the utilization rate of sputtering targets.