In this study, β-1,3-xylanase (Xyl3088) was designed and prepared by constructing the expression vector plasmid and expressing and purifying the fusion protein. β-1,3-xylo-oligosaccharides were obtained through the specific enzymatic degradation of β-1, 3-xylan from Caulerpa lentillifera. The enzymolysis conditions were established and optimized as follows: Tris-HCl solution 0.05 mol/L, temperature of 37 °C, enzyme amount of 250 μL, and enzymolysis time of 24 h. The oligosaccharides' compositions and structural characterization were identified by thin-layer chromatography (TLC), ion chromatography (IC) and liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS). The IC50 values for scavenging 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2-azino-bis-3-ethyl-benzothiazoline-p-sulfonic acid (ABTS+), and superoxide anion radical (•O2−) were 13.108, 1.258, and 65.926 mg/mL for β-1,3-xylo-oligosaccharides, respectively, and 27.588, 373.048, and 269.12 mg/mL for β-1,4-xylo-oligosaccharides, respectively. Compared with β-1,4-xylo-oligosaccharides, β-1,3-xylo-oligosaccharides had substantial antioxidant activity and their antioxidant effects were concentration dependent. β-1,3-xylo-oligosaccharides also possessed a stronger anti-inflammatory effect on RAW 264.7 cells stimulated by lipopolysaccharide (LPS) than β-1,4-xylo-oligosaccharides. At a working concentration of 100 μg/mL, β-1,3-xylo-oligosaccharides inhibited the release of NO and affected the expression of IL-1β, TNF-α, and other proteins secreted by cells, effectively promoting the release of pro-inflammatory mediators by immune cells in response to external stimuli and achieving anti-inflammatory effects. Therefore, β-1,3-xylo-oligosaccharides are valuable products in food and pharmaceutical industries.