Biofloc technology (BFT) is a new green culture technology that is intended not merely to eradicate nitrogenous residues but also enhance immunity and antioxidant activity in aquatic animals. A 56-day feeding trial and a 96 h ammonia challenge test were implemented to evaluate the effect of acute exposure to ammonia and BFT alterations on Rhynchocypris lagowski: digestive enzyme, inflammation response, oxidative stress and immunological parameters in zero water exchange tanks. According to the differences of C/N ratios, the experiment was divided into four groups: C/N 10.8:1 (control group), C/N 15:1, C/N 20: 1 and C/N 25:1. The results provided evidence that weight gain rate (WGR), specific growth rate (SGR) and protein efficiency ratio (PER) were significantly elevated in C/N 20, while food conversion rate (FCR) was considerably decreased (P < 0.05) compared to the control. Significant increases in digestive enzyme amylase (AMS), lipase (LPS), protease (PRS) and cellulase (CES) activity; Immune enzyme complement C3, complement C4, Nitric Oxide Synthase (NOS) and immunoglobulin M (IgM) activity; Serum biochemical lysozyme (LSZ), glutamic pyruvic transaminase (GPT), glutamic oxaloacetic transaminase (GOT) and alkaline phosphatase (AKP) activity; Inflammation TNF-α, IL-1β, IL-2, IL-6 of R. lagowskis were found in the C/N 20 group after a 56-day feeding trial and a challenging trial (P < 0.05). Comparing the antioxidant capacity of R. lagowski in gills, brains and spleen of juveniles from the four experimental groups, the activity of superoxide dismutase (SOD), total antioxidant capacity (T-AOC), catalase (CAT) activity and glutathion reductases (GR) activity of juveniles in the C/N 20 group were significant higher (P < 0.05), and the content of malondialdehyde (MDA) was considerably lower than that in the control. Overall, these findings suggest that BFT not only can enhance R. lagowski growth performance, digestive enzyme activity, and strengthen antioxidant status but also upgrade immune response, improve the ability of resistance to ammonia stress.