Background Previous studies have shown that feeding a high‐energy formula (HF) to infants after cardiac surgery increases energy intake, with fewer side effects on cardiopulmonary function. However, impacts on weight gain and gastrointestinal function remain unclear. Aims and objectives To determine the impact of HF compared with standard formula on weight gain and gastrointestinal tolerance in postoperative infants with congenital heart disease. Design This was a randomized controlled trial. Methods The setting of the study was at a 20‐bed cardiac intensive care unit at a tertiary children's hospital in China. Study population included infants <1 year of age who underwent cardiac surgery and were allocated to the intervention group (n = 32) or control group (n = 32). The intervention group received HF (100 kcal/100 mL), and the control group received standard formula (67 kcal/100 mL) for 7 days during the stabilized postoperative period at the cardiac intensive care unit. Primary outcomes were weight gain and gastrointestinal intolerance. Secondary outcomes were energy intake and standard intensive care characteristics. Results Infants who received HF (n = 30) showed less weight loss than those who received standard formula (n = 29); −16 g [95% confidence interval (CI): −74 to 42] versus −181 g (95% CI: −264 to −99), P = 0·001. The evaluation of gastrointestinal intolerance showed that the intervention group had several side effects, such as abdominal distension (n = 1), gastric retention (n = 2) and diarrhoea (n = 1), while the control group had no problems. Enteral energy intake in the intervention group was higher than the control group from day three. Conclusion Infants after cardiac surgery fed with HF gained more weight but had increased feeding intolerance. However, the feeding intolerance symptoms could be relieved by medication and did not affect feeding advancement. Relevance to clinical practice Paediatric intensive care clinicians should consider gradually increasing the energy density of the formula during feeding and assess feeding intolerance signs in some children with malnutrition after cardiac surgery.