Objective: To investigate the application effect of dual sided blue light combined with probiotic preparations on neonatal hyperbilirubinemia and its impact on intestinal microbiota balance. Methods: A total of 98 children with hyperbilirubinemia admitted to the neonatology department of our hospital from June 2022 to June 2025 were prospectively selected and randomly divided into two groups in a 1:1 ratio, with 49 cases in each group. The control group was treated with double-sided blue light therapy, while the experimental group was treated with a combination of double-sided blue light and probiotic preparations. The clinical efficacy of the two groups was compared. Before treatment and 7 days after treatment, the serum total bilirubin (TBIL) level was detected by vanadate oxidation method, and the decline rate of bilirubin was calculated. The intestinal flora index by real-time fluorescent quantitative PCR was used to compare the phototherapy duration, jaundice subsided time and weight growth rate. Results: The total effective rate of the experimental group was 95.92%, which was higher than the control group"s 81.63% (P<0.05); After treatment, the serum TBIL of both groups decreased, with the experimental group lower than the control group. The rate of bilirubin decrease increased, with the experimental group higher than the control group (P<0.05); After treatment, the diversity index of bifidobacteria and gut microbiota (Shannon) in the experimental group was higher than before treatment, higher than the control group, lower than before treatment for Escherichia coli, and lower than the control group (P<0.05); The duration of phototherapy and jaundice resolution time in the experimental group were lower than those in the control group, and the rate of weight gain was higher than that in the control group (P<0.05). Conclusion: Double sided blue light combined with probiotic preparations has significant therapeutic effects on newborns with hyperbilirubinemia, which can improve bilirubin metabolism levels, enhance gut microbiota structure and diversity, shorten the duration of phototherapy, promote jaundice resolution, and increase the rate of weight gain in children.