This study was carried out to evaluate the effects of three Chinese herbal medicines (CHMs) on rumen fermentation, methane emission and population of ruminal microbes using an in vitro gas production technique. Three healthy wethers of Dazu Black goats with similar bodyweights and permanent rumen fistulae were utilized as donors of ruminal fluid. The three botanical medicines were cablin patchouli herb (CPH), atractylodes rhizome (AR) and Amur cork tree (AC). Each CHM was added at a level of 25 g/kg to the substrate dry matter. In vitro gas production was recorded, and methane concentration was determined at 12 and 24 hours of incubation. After 24 hours, the incubation was stopped, and the inoculants were measured for pH, ammonia nitrogen and volatile fatty acids (VFAs) concentrations. Total deoxyribonucleic acid of ruminal microbes was extracted from the inocula, and populations were determined by a real-time quantitative polymerase chain reaction. Populations of total rumen methanogens, protozoa, total fungi, Ruminococcus albus, Fibrobacter succinogenes and Ruminococcus flavefaciens were expressed as a proportion of total rumen bacterial 16S ribosomal deoxyribonucleic acid. Compared to the control, CPH decreased gas production and methane production at 12 and 24 hours of incubation, and inhibited methanogens and total fungi growth. AR decreased acetate to propionate ratio, and methanogens and total fungi populations, but increased propionate molar proportion. AC decreased total VFA concentration, acetate to propionate ratio, gas production at 12 and 24 hours of incubation, methane production at 12 and 24 hours of incubation, and methanogens and total fungi growth, but increased the propionate molar proportion. In conclusion, CPH and AC both suppressed methanogenesis significantly, and the suppression was mediated primarily via the direct action against the rumen microbes involved in methane formation. AC also indirectly abates methane release by occupying the hydrogen (H2) normally utilized for methanogenesis.