This manuscript reports the extraction and characterization of two novel pectin-like polysaccharides, GRP40-F1 and GRP75-F1, from the Gastrodiae rhizome, and explores their potential as anti-inflammatory agents. The molecular weights of GRP40-F1 and GRP75-F1 were estimated to be 4.71 × 106 and 3.28 × 106 Da, respectively. Both polysaccharides were found to be primarily composed of rhamnose, galactose, glucose, mannose, and galacturonic acid in varying molar ratios. Methylation and NMR analysis revealed the presence of 4)-α-D-GalpA-(1→, Glcp-(1→, →2)-Rhap-(1→, and →2,6)-D-Manp-(1→ glycosidic residues in both polysaccharides. In vitro assays demonstrated that GRP40-F1 and GRP75-F1 significantly alleviated inflammation by inhibiting nitric oxide (NO) and prostaglandin E2 (PGE2) production in LPS-activated macrophages (RAW 264.7), with NO inhibition IC50 values of 90.89 μg/mL and 86.80 μg/mL, respectively. Furthermore, GRP75-F1 was found to significantly inhibit the activated MAPK signaling pathway in RAW 264.7 cells by down-regulating the expression of p-p38, p-ERK, and p-JNK in a dose-dependent manner, without affecting p38, ERK, and JNK expression levels. These findings suggest that the pectin-like polysaccharide fractions from Gastrodiae rhizoma possess strong anti-inflammatory properties, and may be key bioactive components contributing to the rhizome's anti-inflammatory effects.