To investigate the effects of feeding frequency on the growth, intestinal health, and metabolism of larval red-tailed catfish () cultured in land-based circular tanks, a 56-day feeding trial was conducted. A total of 450 fish (8.47 ± 0.36 g) were randomly allocated to three feeding frequencies: twice (F2), three times (F3), and four times (F4) daily. The results revealed that the F3 group had a significantly better feed conversion rate, specific growth rate, and weight gain rate compared to the F4 group ( < 0.05). Lipase activity and villus height were also significantly greater in the F3 group compared to the other groups ( < 0.05). The transcriptome of the F3 group showed significant enrichment in immune- and metabolism-related pathways. Additionally, the F3 group had a higher abundance of beneficial compared to the other groups. was identified as the main contributor in the F3 group, and its abundance was significantly decreased in the F4 group ( < 0.05). These findings indicated that a feeding frequency of three times per day improves the growth performance of in aquaculture by increasing the abundance of beneficial Clostridium and Plesiomonas, activating multiple immune pathways, and enhancing amino acid metabolism.