Objective Exploring the effects of five-element music on depressive behavior and gut flora of stress-phobic offspring during pregnancy. Methods Thirty-six 0.5-day pregnant Wistar female rats were randomly divided into the blank group, the stress-phobic group and the five-element music group, and the litters were continued in the maternal group. Pregnant rats in the 1-19 day gestation stress-phobic group and the five-element music group were modeled by the side-by-side electroshock method, while the five-element music group was given the five-element music feathering intervention. The effect of modeling was evaluated by using the absent field experiment, enzyme-linked immunosorbent assay (ELISA) to detect the fearful behavior and serum glucocorticoid (GC) content of the pregnant rats on the 20th day of gestation; the depressed mood of the rats was evaluated by using the absent field experiment, the tail-hanging experiment and the sugar-water preference experiment at the age of 3 weeks; and the changing pattern of the intestinal flora of the rats was analyzed by using 16S rRNA sequencing. Results Compared with the blank group, pregnant rats in the stress-phobic group stayed longer in the peripheral area of the absent field, had fewer entries into the central area (p < 0.05), and had higher serum GC levels (p < 0.001), whereas the five-element music group reversed the behavioral changes in the stress-phobic group (p < 0.05) and the serum GC levels (p < 0.001). Compared with the blank group, the stress-phobic group showed a decrease in the number of absentee grids worn (p < 0.01), a decrease in the glycemic index, and a prolongation of the time of tail suspension (p < 0.05), while the five-element music group showed an increase in the number of absentee grids worn, the glycemic index, and a shortening of the time of tail suspension (p < 0.05), and the total distance traveled by the rats in each group did not show any significant difference. The intestinal flora species diversity of the rats in the stress-phobic group decreased (p < 0.01) and the structure of the flora was significantly changed compared with that of the blank group, in which the abundance of Proteobacteria, Enterobacteriaceae, Enterococcus and Escherichia were up-regulated, and the abundance of Spirochaetes and Spirochaetaceae, Lachnospiraceae, Ruminococcaceae,Treponema, Prevotella,Coprococcus, Allobaculum, Ruminococcaceae_Ruminococcus, Dorea was down-regulated, and five-element music group of littermates showed an increase in species diversity of the intestinal flora compared to the stress-phobic group (p < 0.01) and reversed the changes in the abundance of the above flora. Conclusion A five-element music intervention during pregnancy is effective in ameliorating fearful stress-induced depression behavior and gut flora disruption in offspring during pregnancy.