Various Fe-vacancy orders have been reported in tetragonal Fe1-xSe single crystals and nanowires/nanosheets, which are similar to those found in alkali metal intercalated A1-xFe2-ySe2 superconductors. Here we report the in-situ angle-resolved photoemission spectroscopy study of Fe-vacancy disordered and ordered phases in FeSe multi-layer thin films grown by molecular beam epitaxy. Low temperature annealed FeSe films are identified to be Fe-vacancy disordered phase and electron doped. Further long-time low temperature anneal can change the Fe-vacancy disordered phase to ordered phase, which is found to be semiconductor/insulator with (root 5) x (root 5) superstructure and can be reversely changed to disordered phase with high temperature anneal. Our results reveal that the disorder-order transition in FeSe thin films can be simply tuned by vacuum anneal and the (root 5) x (root 5) Fe-vacancy ordered phase is more likely the parent phase of FeSe.