To explore the clinical efficacy of early micro feeding combined with intestinal probiotics for treating neonates with feeding intolerance. Methods: 90 neonates with feeding intolerance were selected and were divided into two groups (45 cases in each group) according to the random number table method from January 2020 to February 2022. The neonates in the control group were treated with routine feeding, and the neonates in the study group were treated with early micro feeding combined with intestinal probiotics. The treatment effect of the neonates in the two groups were observed and recorded. The values of the serum biochemical indexed of the neonates in the two groups before and after treatment were detected. Results: After treatment, the durations of vomiting (2.7±0.7d), the abdominal distension (2.8±0.9d), and the total gastrointestinal feeding (6.7±1.6d), the time to the recovery of birth weight (5.4±1.2d), and the hospitalization time (12.9±1.7d) of the neonates in the study group were significantly shorter than those (3.6±0.9d, 4.0±1.2d, 7.9±1.7 d, 6.0±1.3 d, and 14.6±2.0 d) of the neonates in the control group. The serological indexes of the neonates in both groups after treatment had improved significantly. The levels of serum total bilirubin (81.43±27.12μmol/L) of the neonates in the study group was significantly lower than that (107.75±32.08μmol/L) of the neonates in the control group. The levels of albumin (43.08±10.25 g/L) and prealbumin (18.65±1.25 mg/dl) of the neonates in the study group were significantly higher than those (36.34±9.20 g/L and 13.40±1.15 mg/dl) of the neonates in the control group (all P＜0.05). Conclusion: Early microfeeding combined with intestinal probiotics for treating the neonates with feeding intolerance can effectively promote the maturation of their gastrointestinal tract, shorten the time of their parenteral nutrition, and improve their nutritional indicators of the serum biochemistry detection