Background The benefits of probiotics being used in animals are well-documented via evidenced growth performance improvement and positive modulations of gut microbiota (GM). Thus, a combination of effective microorganisms (EM) has been frequently used in animal production, including broilers. However, there are only very limited reports of EM on the growth performance and the modulation in GM of partridge shank broiler chicks. Methods We attempted to evaluate the effects of a basal diet with the addition of an EM mixture on the growth performance and gut microbiome of the chicks. A total of 100 ten-day-old female partridge shank broiler chicks were randomly divided into two groups of 50 chicks each, of which, one group fed with EM supplementation in the basal diet (designated as EM-treated group), the other group just fed with a basal diet (referred as to non-EM treated group or control group). The body weight, daily feed intake, daily gain, feed conversion ratio and other growth parameters were observed and compared between EM-treated and non-EM-treated chicks, and the gut microbiota was profiled by 16S rRNA-based next generation sequencing (NGS). Results EM-treated chicks showed significantly increased performances in body weight (BW), average daily gain (ADG) and reduced feed conversion ratio (FCR). Histological observation indicated that dietary supplementation of EM significantly increased the villus heights (VH) and the ratio of villus height to crypt depth (VH/CD), while decreased the CD of jejunum, ilea, and ceca. The results of 16S rRNA-based gut microbiota analyses showed that Firmicutes accounted for the most of the relative abundance (63.24%∼92.63%), followed by Proteobacteria (0.62%∼23.94%), Bacteroidetes (0.80%∼7.85%), Actinobacteria (0.06%∼13.69%) and others in both EM-treated and non-EM-treated broiler chicks. The addition of EM could not alter the alpha diversity of gut microbiota. Compared with the non-EM-treated chicks, the abundances of bad bacteria in the phyla of Firmicutes, Euryarchaeota, and Ruminococcus were dramatically decreased in that of EM-treated chicks, while the abundances of good bacteria in the phyla of Actinobacteria and WPS-2 were significantly increased. Conclusions The supplementation of EM in feed could improve the growth performance and positively influence the morphological characteristics of the intestine, and ameliorate the community and structure of the intestinal microbiota of partridge shank broiler chicks.