To study the regulation and feedback mechanism of cholecystokinin and trypsin in black bream, Megalobrama pellegrini (Tchang, 1930) 60 days after hatching under 15 days short-term fasting and different feeding frequencies within 24 hours during the same period, M. pellegrini (wet weight 183.75 ± 61.16 mg, total length 20.74 ± 4.08 mm) developed in a recirculating aquaculture system were selected as the subject. In the short-term fasting trial, the body weight, trypsin, and CCK of the feeding control group (FCG) were higher than those of the fasting test group (FTG). Trypsin and CCK in FTG reached the lowest value on the ninth day and the CCK content reached the highest value on the 11th day. A negative feedback regulation of CCK and trypsin had not been found in this trial. The degree of damage to intestinal chorionic epithelial cells was higher than that of hepatopancreas, and detachment of epithelial cells and the striatal border was the main damage. In the 24-hour daily rhythm experiment, juvenile fish were randomly assigned to (A) once feeding, (B) twice feeding, (C) three times feeding, (D) fasting. CCK showed a minimum value at 1:00+ in group A, while a peak occurred at night in group B\C\D and a maximum value in group C, and a single satiety stimulus can lead to increased hunger. The four treatment groups had an apparent closed-loop regulation while the control point of the fasting group (D) shifted forward to the next day. Different feeding frequencies in a single day had no direct effect on the long-term fluctuation of CCK and trypsin diurnal rhythm. Feeding three times a day was beneficial to the individual growth of juvenile M. pellegrini, a better growth results may be produced in the long term. This study aimed to provide a reference for the feeding strategy of juvenile M. pellegrini in the RAS.