A layer-controlled two-dimensional (2D) molybdenum disulfide (MoS2) film with tunable bandgaps is highly desired for the fabrication of electronic/photoelectronic devices. In this work, we demonstrate that a focused ion beam (FIB) can be applied to thin MoS2 films layer-by-layer. The layer number can be controlled by simply changing the Ga(+) beam exposure time and the thinning speed is about half a layer per second. OM, AFM, PL and Raman spectra were used to monitor the change of layer numbers and characterize the morphology, thickness, and homogeneity of MoS2 films. The FIB layer-by-layer thinning technology will establish a new methodology for rationally thinning all kinds of 2D layered materials.