External　environments　to　microbial　eukaryotic　communities　often　change　gradually　with　time.　However,　whether　the　responses　of　microbial　eukaryotic　communities　to　these　gradually　changed　environments　are　continuous　or　hysteretic　and　the　mechanisms　underlying　these　responses　are　largely　unknown.　Here,　we　used　a　microcosm　to　investigate　the　temporal　variation　of　microbial　eukaryotic　communities　with　the　gradually　decreased　nutrient　concentrations　(nitrogen　and　phosphorus).　We　found　the　differences　of　microbial　eukaryotic　community　composition　and　species　richness　between　the　control　and　treatment　groups　were　low　during　the　days　0　to　12,　although　the　nutrient　concentrations　decreased　rapidly　during　this　period　in　treatment　group.　However,　these　differences　were　clear　during　the　days　14　to　18,　although　the　nutrient　concentrations　decreased　slowly　during　this　period　in　treatment　group.　The　mechanisms　for　these　results　are　that　the　strong　homogenous　selection　(perhaps　due　to　the　biotic　factors)　during　the　days　8　to　10　in　treatment　group　might　enhance　the　stability　of　microbial　eukaryotic　communities.　However,　the　continuously　decreased　nutrient　concentrations　weakened　the　homogenous　selection　and　promoted　the　strength　of　environmental　filtering,　and　therefore　resulted　in　the　distinct　change　of　microbial　eukaryotic　communities　during　the　days　14　to　18　in　treatment　group.　Fungi,　Chlorophyta　and　Chrysophyta　which　associated　with　the　nutrient　removal　played　important　roles　in　this　hysteretic　change　of　microbial　eukaryotic　communities.　Overall,　our　findings　suggest　that　disentangling　the　non-linear　response　of　communities　to　gradual　environmental　changes　is　essential　for　understanding　ecosystem　restoration　and　degradation　in　future.　©　2019,　Springer　Science+Business　Media,　LLC,　part　of　Springer　Nature.