To observe the effect of probiotics on the stress responses and intestinal permeability of term neonates with low Apgar scores, the present study retrospectively analyzed the clinical data of 78 term neonates (42 males and 36 females). In the control group (n=38), total parenteral nutrition and comprehensive treatment (anti-infection therapy) were provided. In the observation group (n=40), the neonates were administered Lactobacillus Complex Capsules in addition to the control group treatment. The corticotropin-releasing factor level was determined using ELISA; cortisol levels were determined using a radioimmunoprecipitation assay; D-lactate and diamine oxidase levels were determined using ultraviolet spectrometry; procalcitonin levels were determined using ECL; and C-reactive protein levels were determined using a protein analyzer. Following treatment, the levels of all parameters were lower in the observation group compared with the control group, and the differences were statistically significant (P<0.05). In the observation group, the daily milk intake was 16.57±2.58 ml, which was significantly higher than that of the control group (13.26±1.87 ml), while the length of hospital stay and total parenteral nutrition time, which were 12.31±2.02 and 6.21±1.26 days, respectively, in the observation group, were significantly shorter than those of the control group (14.86±2.58 and 8.86±1.78 days, respectively), and the differences were statistically significant (P<0.001). The results of the present study suggested that probiotics can ameliorate the stress response and intestinal permeability of term neonates with low Apgar scores, thereby, facilitating gastrointestinal function recovery.