Recent studies on germ-free mice show that intestinal methanogens may be closely associated with host's adipose metabolism. The present study aimed to investigate effects of inhibition of intestinal methanogen populations on host fat metabolism by establishing a healthy Sprague Dawley (SD) rat model through the intragastric administration of bromochlordomethane (BCM). Forty-five 8-week old healthy male SD rats were randomly divided into five groups including one control and four BCM treatments. The experiment lasted 60 days with two separate 30-day experimental periods. At the end of first period, three BCM treatment groups were further used: one group continued with BCM treatment, one group stopped with BCM treatment, and the other one inoculated with faecal mixture of methanogens from rats. Results showed that the methanogen population in feces was reduced sixfold with no effect on the bacterial community by daily dosing with BCM. Daily gain, epididymal fat pad weight, levels of plasma low-density lipoprotein and cholesterol were significantly higher in the BCM-treated animals, while the high-density lipoprotein was lower than that of the control. The expression of PPARγ, LPL, PP2A, SREBP-1c, ChREBP, FASN and adiponectin genes in BCM treatment group was universally upregulated, while the expression of Fiaf gene was downregulated. After termination of BCM treatment and followed either with or without re-inocubation with faecal methanogen mixture, the rats had their faecal methanogen populations, blood parameters and gene expression returned to the original level. Results suggest that regulation of gut methanogens might be a possible approach to control host body weight.