Abstract: The yellowcheek carp (Elopichthys bambusa) is a large and aggressive carnivorous fish. Weaning represents a significant bottleneck in the large-scale aquaculture of yellowcheek carp. To investigate the appropriate timing for weaning and its effects on growth and intestinal health, 15 days post-hatching (dph) weaning group (W15), a 22 dph weaning group (W22), and a 29 dph weaning group (W29) were set up to wean yellowcheek carp at 15 dph, 22 dph, and 29 dph, respectively. We investigated the effects of weaning starting time on growth, survival, and intestinal development. The results showed that the total length, body weight, and survival rate of juvenile yellowcheek carp in the W22 and W29 groups were significantly higher than that in the W15 group at different periods. Additionally, intestinal villus height and muscle thickness were significantly higher in the W22 and W29 groups compared to the W15 group. At 36 dph, the W22 group exhibited the highest specific growth rate, while the W29 group had the highest survival rate. During the weaning period, when the prey’s body depth equaled the predator’s mouth width, the predator’s total length was approximately 1.5 times the prey’s total length, described by the relationship TL_prey=0.53×TL_predator+3.63. Moreover, the trypsin activity in the fast-growing (FB) group of juvenile yellowcheek carp was significantly higher than that in the slow-growing (FS) group, whereas the activity of amylase, lipase, and alkaline phosphatase were significantly lower. Deferentially expressed genes in the FB and FS groups were significantly enriched in lipid metabolic pathways, including the PPAR signaling pathway, fatty acid metabolism, and fatty acid biosynthesis. qPCR confirmed significant differences in the expression of four lipid metabolism-related genes: FABP7, FAS, CPT1, and GYS2. The results indicated that initiating weaning at 22—29 dph can obtain the best growth and survival outcomes. Additionally, selecting larger individuals, approximately 1.5 times the average length of the population, can prevent cannibalism and improve survival rate during weaning. The growth performance of juvenile yellowcheek carp post-weaning may be linked to differences in intestinal digestive enzyme activities and lipid metabolism ability. This study provides important guidance for the weaning and post-weaning cultivation of juvenile yellowcheek carp and may inform weaning research for other carnivorous fish species.