A 75 days experiment was conducted in a flow-through system on juvenile gibel carp (Carassius auratus gibelio) (3.43 ± 0.01 g) to evaluate the effects of dietary lysozyme on growth performance, intestine morphology, microbiota and immune response. Four isonitrogenous (crude protein: 367 g kg−1) isolipid (62 g kg−1) and isocaloric (gross energy: 17.92 kJ g−1) diets were formulated to contain 0, 100, 500 and 1000 mg kg−1 lysozyme, respectively. The results showed that specific growth rate (SGR) and feed efficiency (FE) increased at 1000 mg kg−1 lysozyme. Blood leucocyte phagocytic activity (PA) and serum lysozyme (LZM) decreased with dietary lysozyme on day 25, 50 and 75. There were no significant differences in alternative complement pathway (ACP), respiratory burst (ROS), serum superoxide dismutase (SOD), glutathione peroxidase (GSHpx) or malonaldehyde (MDA). After Aeromonas hydrophilia challenge, higher survival was obtained at 500 mg kg−1 group. PA, ROS, SOD, LZM and ACP increased with increasing dietary lysozyme, while MDA reversed. Goblet cells in mid-intestine and microvilli height in distal intestine increased with dietary lysozyme on day 75. Dietary lysozyme reduced the diversity of intestine microbiota. In conclusion, oral administration of 500 mg kg−1 dietary lysozyme for 75 days is recommended for the survival of gibel carp and 1000 mg kg−1 dietary lysozyme for fast growth.