Nannochloropsis is widely used in aquaculture as a feed source. However, large-scale cultivation of Nannochloropsis usually fails due to rotifer contamination. In order to identify an effective technique for reducing rotifer contamination, the effect of Brachionus plicatilis contamination on photosynthetic characteristics in Nannochloropsis oculata and the efficacy of the celangulin (CA):toosendanin (TSN) (1:9) combination for rotifer extermination were investigated using chlorophyll a fluorescence transient. B. plicatilis could directly devour microalgal cells and sharply reduced N. oculata density to very low levels. B. plicatilis also inhibited activities of PSII reaction centers, both acceptor and donor side, thereby damaging the photosynthetic performance of surviving N. oculata cells. However, the CA:TSN (1:9) combination could completely eliminate B. plicatilis, thereby preventing rotifers from devouring microalgae cells and protecting the photosynthetic performance of the surviving algal cells against rotifers damage. Therefore, the binary combination of CA:TSN (1:9), is considered to be a good candidate of botanical pesticide for controlling rotifer contamination.