In this paper, conventional continuous epitaxial growth and metal modulated epitaxial (MME) growth of AlN were investigated with the plasma-assisted molecular beam epitaxy (PA-MBE) system. It is difficult to control the growth mode of the conventional continuous epitaxial growth method, in which excessive Al-rich and N-rich growth modes easily occur, and also a slightly Al-rich growth mode is accompanied by the appearance of some pits, leading to rough surface morphology. However, the growth mode of AlN films is easier to control by MME method, by which AlN films with good morphology can be fabricated by adjusting the supply time of Al and N sources. The optimized MME solution is proposed as follows: firstly, opening the Al source shutter for 30 s, then opening the Al and N source shutters for 60 s, and finally opening the N source shutter alone for 72 s, the ratio of Al source shutter opening time to N source shutter opening time of a single cycle is 0.7. Almost pits-free AlN films with a low roughness of 0.3 nm (2 μm×2 μm) are fabricated after 40 cycles.