Objective: To investigate the influence of family integrated care (FICare) on the intestinal microbiome of preterm infants in neonatal intensive care unit (NICU). Methods: This was a prospective observational pilot study. A total of 44 preterm infants (23 boys, 52%) admitted to NICU of the Third Xiangya Hospital of Central South University from July, 2015 to June, 2017 were enrolled and divided into FICare, non-FICare groups. Totally 20 term infants (11 boys, 55%) were enrolled into control group, who were sent to the Pediatric Healthcare Clinic for regular health check on postnatal 28-31 days. All infants were free from probiotics after birth and on full enteral feeding. Clinical data of all infants were collected. Two fresh stool specimens of infants in FICare group were collected after 2 weeks of FICare implementation, without use of antibiotics during the prior 1 week. Stool specimens of infants in non-FICare group were collected at the meantime;while for the infants in control group, stool samples were collected at 4 weeks of age. All specimens were stored in-80 ℃ freezer, subsequently investigated by 16 S rRNA sequencing. The results were filtered by paired-end reads software based on RNA overlapping-splicing and tags calculation. Operational taxonomic units (OTU) were analyzed for intestinal microbiome richness. Intestinal microbiome diversity was measured with Shannon index. One-way ANOVA or Kruskal-Wallis H statistic analysis or Chi-square test was used for statistical analysis. Results: There were no significant differences among FICare, non-FICare and control groups in male proportion (52% (11/21) vs. 52% (12/23) vs. 55% (11/20), χ(2)=0.041, P=0.980), in-born ratio (90% (19/21) vs. 87% (20/23) vs. 85% (17/20), χ(2)=0.000, P=1.000), and percentage of infants with Apgar scores<7 at 5 minutes after birth (14% (3/21) vs. 9% (2/23) vs. 5% (1/20), χ(2)=0.120, P=0.729). Similarly, no significant differences were found between FICare and non-FICare groups in terms of gestational age ((29.7±1.8) vs. (29.9±1.7) weeks, t=0.378, P=0.707), birth weight ((1 266±310) vs. (1 326±318) g, t=0.631, P=0.531), median age of initiating feeds (4 vs. 4 days old, Z=0.666, P=0.505), and median age of achieving feeding volume of 120 ml/(kg·d)(13 vs. 11 days old, Z=1.014, P=0.310). However, the breast-feeding rate in FICare group (18/21, 86%) was significantly higher than that in non-FICare group (8/23, 35%) (t=11.780, P=0.001). The medium Shannon index was 0.72 (0.27,2.66), 0.61 (0.18,1.83), and 0.52 (0.08,1.71) in control, FICare, and non-FICare groups, respectively, without significant difference (H=1.823, P=0.402). The domain flora was Lactobacillus Firmicutes in all three groups, which was of the highest percentage in FICare group (71.6±5.4)%, followed by control group (65.4±6.6)% and non-FICare group (55.6±8.8)%, with a significant difference (F=27.919, P=0.000). Conclusions: FICare can improve the richness and diversity of intestinal microbiome, stimulate the establishment of flora close to those of normal breast-feeding infants in preemies in NICU, making its establishment being more similar to normal term breast-feeding infants. This effect might be caused by the increased skin-to-skin contact and increased fresh breast-milk-feeding in FICare.