Few studies have examined the effects of feeding total mixed ration (TMR) versus roughage and concentrate separately (SF) on ruminant methane production. Therefore, this study compared differences in methane production, ruminal characteristics, total tract digestibility of nutrients, and rumen microbiome between the two feeding methods in Holstein steers. A total six Holstein steers of initial bodyweights 540 ± 34 kg were divided into two groups and assigned to a same experimental diet with two different feeding systems (TMR or SF) in a crossover design with 21 d periods. The experimental diet contained 73% concentrate and 27% forage and were fed twice a day. The total tract digestibility of crude protein, neutral detergent fibre, and organic matter were not affected by the two different feeding systems. Steers fed TMR emitted more methane (138.5 vs. 118.2 L/d; P < 0.05) and lost more gross energy as methane energy (4.0 vs. 3.5% gross energy intake; P = 0.005) compared to those fed SF. Steers fed TMR had greater (P < 0.05) total volatile fatty acid (VFA), ammonia-N concentrations and propionate proportion of total VFA at 1.5 h, whereas lower after that compared to steers fed SF. The greater (P < 0.05) acetate: propionate ratio at 4.5 h for steers fed TMR reflected the shift of H2 sink from propionate towards acetate synthesis. The lower (P < 0.05) isobutyrate and isovalerate proportions of total VFA observed in steers fed TMR implies decrease in net consumption of H2 for microbial protein synthesis compared to SF. There were no differences in both major bacterial and archaeal diversity between TMR and SF, unlike several minor bacterial abundances. The minor groups such as Coprococcus, Succiniclasticum, Butyrivibrio, and Succinivibrio were associated with the changes in ruminal VFA profiles or methanogenesis indirectly. Overall, these results indicate that SF reduces methane emissions from ruminants and increases propionate proportion of total VFA without affecting total tract digestion compared to TMR. There were no evidences that the response differed due to different major underlying microbial population.