Objective To evaluate the clinical value of functional ultrasound for early warning of feeding intolerance (FI) in preterm infants. Methods A prospective cohort analysis was performed in 107 preterm infants (FI group, n=48; non-FI group, n=59). Functional ultrasound was used to assess gastric emptying time, intestinal peristalsis frequency, and intraluminal gas-liquid abnormalities. Results Compared with the non-FI group, the FI group had a significantly prolonged gastric emptying time [(46±8) min vs (36±7) min, P<0.001], a reduced intestinal peristalsis frequency [(8.8±2.0) times/5 min vs (12.4±3.3) times/5 min, P<0.001], and a higher rate of moderate or greater gas-liquid abnormalities (63% vs 20%, P<0.001). A multivariable logistic regression model based on three functional ultrasound parameters—gastric emptying time, intestinal peristalsis frequency, and intestinal gas-liquid interface score—achieved an area under the receiver operating characteristic curve (AUC) of 0.910 (sensitivity 79.2% and specificity 93.2%). Internal validation (AUC=0.911, 95%CI: 0.845-0.964) and external validation (AUC=0.904, 95%CI: 0.854-1.000) both showed high predictive performance. Subgroup analyses indicated that the model retained good predictive ability across gestational age and birth weight groups. Conclusions Functional ultrasound can detect intestinal dysfunction before clinical manifestations of FI. The combined parameter model can be used for FI risk assessment and individualized feeding management in preterm infants, with high clinical applicability and potential for broader implementation.