Background Changes in the intestinal flora composition is referred to as dysbiosis, which is related to obesity development, thus supporting the potential roles of nutrients acting on intestinal flora to exert salutary effects on energetic metabolism of host. Dietary fiber has been known to affect the composition of intestinal flora. The aim of the present study was to investigate the functional effects of konjac flour (KF) on obesity control in respect to improving inflammation, metabolism, and intestinal barrier function, and the possible association of the effects with intestinal flora composition changes. Methods Mice (n = 30) were randomly divided into control group (n = 10), high-fat-diet (HFD) group (n = 10), and KF intervention group (n = 10), followed by feeding for 12 weeks and with adding a KF daily supplementation for the treatment group. Body weight, fat accumulation, inflammation, and energetic metabolism markers in multiple tissues and the gut microbiota of the mice were examined at the end of the experiment. Results The KF supplementation significantly reduced the gains in weight, fat mass, as well as adipocyte size of HFD mice and lowered the serum TC, leptin (LEP), thiobarbituric acid-reacting substance (TBARS), IL-6, and lipopolysaccharide (LPS) levels in HFD mice. KF also upregulated the expression of intestinal mucosa protein gene Intection and tight junction ZO-1 in HFD mice, as well as upregulate the expression of energy metabolism genes PPAR alpha and CPT-1 as well as the fat metabolism gene HLS in livers and fat tissues, and downregulate that of fat synthesis gene PPAR gamma (p < 0.05). The KF treatment increases the a-diversity and change the n-diversity of the intestinal microflora in HFD mice and boosted the abundances of some obesity-related beneficial microorganisms (such as Megasphaera elsdenii) in the intestinal microflora of HFD mice, while reduced those of harmful microorganisms (such as Alistipes, Alloprevotella, Bacteroides acidifaciens, and Parabacteroides goldsteinii). The abundance of Alistipes was positively correlated with weight, fat mass, serum TC, TG, LEP, IL-6, and LPS contents as well as PPAR gamma gene expression; while notably and negatively related to the expression of CPT-1 and HLS genes (p < 0.01). KF remarkably increased the abundance of Aerococcaceae, while reduced that of Alistipes finegoldii (p < 0.01). Conclusions Supplementation with KF achieves favorable effects on treating obesity, improving inflammatory response, metabolism, and intestinal barrier function, by regulating intestinal microfloral structure in HFD-fed mice.