Obesity is one of the most serious public health challenges. Recently, we found that flaxseed polysaccharides (FPs) had an anti-obesity effect through promoting lipid metabolism, but the obesity-inhibiting pathway of FP is still unclear. In this study, after FP intervention in an obese rat model, a transcriptome study was performed to further investigate how FP intervention alters the gene expression of colonic epithelial tissues (CETs). The results showed that there were 3785 genes differentially expressed due to the FP intervention, namely 374 downregulated and 3411 upregulated genes. After analyzing all the differentially expressed genes, two classical KEGG pathways were found to be related to obesity, namely the PPAR-signaling pathway and energy metabolism, involving genes Fabp1–5, Lpl, Gyk, Qqp7, Pparg, Rxrg, Acsl1, Acsl4, Acsl6, Cpt1c, Car1–4, Ca5b, Car8, Car12–14, Cps1, Ndufa4l2, Cox6b2, Atp6v1g2, Ndufa4l2 and Cox4i2. QRT-PCR results showed a consistent expression trend. Our results indicate that FP promotes lipid metabolism by changing the expression of some key genes of CETs, thus inhibiting obesity.