Fucoidan, a sulfated polysaccharide rich in fucose, is derived from brown algae and marine invertebrates. Multiple bioactivities have been shown with fucoidan, while growing attraction has emerged in its low-molecular-weight (Mw) hydrolysates. Here, the anti-inflammatory effect of fucoidan, low-Mw acidolyzed fucoidan (LMAF, <1.5 kDa), and high-Mw acidolyzed fucoidan (HMAF, 1.5–20 kDa) were investigated in vitro using lipopolysaccharide (LPS)-stimulated Caco-2 and RAW264.7 co-cultures. Fucoidan, LMAF, and HMAF with different structures exhibited varied anti-inflammatory effects. LMAF and HMAF effectively decreased the nitric oxide release of RAW264.7 cells. LMAF exhibited a competitive effect in reducing tumor necrosis factor-alpha, interleukin-1 beta, and interleukin-6 levels compared to HMAF and fucoidan. Transcriptome of RAW264.7 revealed that LPS and LMAF mainly regulated the transcriptional expression of genes, including Tnf, Il6, Il1b, Junb, and Nfkb1 in the TNF signaling pathway, NF-kappa B signaling pathway, and cytokine–cytokine receptor interaction. RT-PCR results indicated that LMAF markedly reduced the LPS-elevated expression of Cxcl2, Tnf, Ccl2, Il1b, and Csf2. Moreover, LMAF effectively increased the proteins expression of Claudin-1, Occludin, and Zonula occluden-1 in Caco-2 cells. This study highlights the potential of LMAF to improve inflammation and intestinal barrier integrity, offering a foundation for further application of low-Mw fucoidan hydrolysates.