Objective To investigate autophagic changes of free-living amoeba during transformation from trophozoites to cysts. Methods Trophozoites were induced to form cysts with withdrawing of E. coli from the medium. Autophagic changes of the amoeba were investigated on 24hours, 36hours and 48hours after induction. the morphological changes of amoeba during encystation were viewed with a scanning electron microscope, The autophagic structures in amoeba were examined with a transmission electron microscope, cross-section areas of the autophagic structures were measured with an image analyzer. The autophagosomes of amoeba were labeled with monodansylcadaverine (MDC) staining and counted under confocal laser scanning microscope. Results In the control group, amoeba was full of fragment of E. coli, the level of autophagy was low. There were few autophagic structures in amoeba. Comparing with the control group, the autophagic level of amoeba after induction for 24 hours was enhanced significantly. Number of autophagic structures increased, the ratios of the cross-sectional areas of the autophagic precursors, autophagosomes and autophagolysosomes to that of the cytoplasm of amoeba were higher. The level of autophagy was attenuated significantly and number of autophagic structures decreased after induction for 36 hours. After induction for 48 hours, 92% trophozoites were transform to cysts, no autophagic structures were observed. Conclusion During encystation, autophagic activities of amoeba increased significantly in the early phase and decreaed in the later phase gradually.