Chicken manure is rich in various nutrients, and it is used to improve the nutritional status of microalgae, which subsequently affects the production and nutrition of rotifers. The investigation of the effect of chicken manure on Chlorella and rotifer cultivation is therefore critical for practical production. Here, to investigate the effects of chicken manure extract (CME) on the continuous culture of the biological bait “Chlorella-rotifer”, different concentrations of CME (Groups 1–5: 0, 5, 10, 15, and 20 mL·L−1, respectively) were added to the culture medium for cultivating Chlorella vulgaris, assessed the growth of C. vulgaris, and the optimal amount of CME for culturing Chlorella was determined; and the effects of the cultured Chlorella as food for rotifer cultivation and fatty acid composition of Chlorella and rotifers were analyzed. In 12 days of continuous culture, no significant difference in Chlorella population density was noted among G3, G4, and G5 (P > 0.05). Following completion of the culturing period, the specific growth rate of Chlorella in G3 (0.14 ± 0.01) and G5 (0.14 ± 0.01) showed no significant difference (P > 0.05), and chlorophyll a (Chl a) content in G3 (3.79 ± 0.06 mg·mL−1) was significantly higher than that in G5 (3.30 ± 0.12 mg·mL−1) (P < 0.05). Hence, we chose G3-cultured Chlorella for rotifer cultivation. In the 120-h rotifer cultivation period, the longevity of G3-bred rotifers (G-CME) (15.06 ± 0.82 d) was significantly more than that of the control group (G-BG11) (13.13 ± 1.27 d) (P < 0.05), and the offspring number of rotifer in G-CME (24.75 ± 3.45) was significantly higher than that in G-BG11 (17.75 ± 3.06) (P < 0.05). Rotifer population density and fecundity were significantly improved by G-CME than by G-BG11. Regarding fatty acid composition, the principal component analysis showed that Chlorella cultured by CME (CME-C) and BG11 (BG11-C) and rotifers that used them as diet (CME-R and BG11-R, respectively) exhibited a variation in principal components, with LC-PUFAs (12.66% ± 0.42%) and n-6 LC-PUFAs (3.99% ± 0.17%) being significantly higher in CME-R than in BG11-R (LC-PUFAs: 9.76% ± 0.81%, n-6 LC-PUFAs: 2.17% ± 0.32%) (P < 0.01). In conclusion, CME can promote the growth and alter the fatty acid composition of Chlorella, thus indirectly improving the growth condition and fatty acid content of rotifers; the optimal amount of CME for the continuous cultivation of the bio-bait “Chlorella-rotifer” was 10 mL·L−1.