Limit-fed high concentrate diet was proposed as an effective method to improve feed efficiency and decrease manure output in heifers’ raising, while the effect on hindgut microbiota was still unclear. Therefore, this study aims to investigate the effects of wide range of dietary forage:concentrate ratios (F:C) on the compositions of fecal bacteria and archaea in heifers. Twenty-four Holstein dairy heifers with similar body condition (8–10 mo old) were assigned into 4 treatments and fed diets with different F:C (80:20, 60:40, 40:60, and 20:80, DM basis). The quantity of diets provided to high concentrate fed groups was restricted so that there was a similar intake of metabolizable energy to low concentrate fed groups. From d 20 to 23, fecal samples were collected from the rectum of heifers at 3-h intervals. At the end of sampling, equal amount of sample of each time point from the same heifer were homogenized, and the subsamples were used for nutrient and volatile fatty acids detection and DNA extraction. The fecal bacterial and archaeal communities were investigated by Illumina sequencing. With increasing dietary concentrate levels, the fecal neutral detergent fiber and acetate contents linearly decreased (P < 0.01), while fecal starch, propionate, and butyrate contents increased (P ≤ 0.05). An increased concentrate level linearly increased (P = 0.02) Proteobacteria abundance, while linearly decreased (P = 0.02) Bacteroidetes abundance in feces. At the genus level, cellulolytic bacteria, namely unclassified Ruminococcaceae and Paludibacter, were linearly decreased (q ≤ 0.02), while non-fibrous carbohydrate degraders, namely Roseburia and Succinivibrio, were linearly increased (q ≤ 0.05). However, the abundance of most detected archaeal were similar across different F:C, and only Methanosphaera were linearly decreased (P = 0.01) with increasing concentrate levels. These results suggest that different F:C diets have significant effects on the fecal bacterial communities, while have slight effect on the archaeal communities. Our study might further be beneficial to enhance the feed digestibility and relieve environment problems in heifers’ rearing.