Funoran and furcellaran were isolated through a successive cascade extraction process, followed by the depolymerization of extracted polymers via an auto-hydrolysis process. The molecular weight and structural peculiarities of both native and partially depolymerized polysaccharides were investigated using size-exclusion chromatography (SEC), FTIR, and NMR spectroscopy. Immunotropic effects of the native and partially depolymerized polysaccharides were explored through various in vitro assays. Although both higher and lower molecular weight funoran exhibited anti-inflammatory activity on LPS-stimulated RAW264.7 cells by significantly downregulating iNOS and COX-2 gene expression, as well as the secretion of pro-inflammatory cytokines, native funoran performed slightly better. Conversely, higher molecular weight furcellaran remarkably activated RAW264.7 cells compared to the non-treated control by inducing inflammatory mediators and pro-inflammatory cytokines, including the anti-inflammatory cytokine IL-10. Lower molecular weight furcellaran was unable to activate the macrophages, showing a similar behavior pattern to funoran samples in LPS-treated cells. Furthermore, the TLR4/NF-κB signaling pathway appears to be modulated by sulfated polysaccharides, leading to both anti-inflammatory and immunostimulatory responses in RAW264.7 cells through blocking and activating mechanisms. These findings indicate that sulfated polysaccharides could be promising therapeutic agents, and indeed, the molecular weight of polysaccharides plays a crucial role in the immune response of RAW264.7 macrophages.