Low-molecular-weight carrageenan (LMWC) has attracted great interest because it shows advantages in solubility, and bioavailability compared to original carrageenan. An environmentally friendly and efficient method for preparing low molecular weight carrageenan is required. In present study, based on the natural phenomenon whereby carrageenan exhibits soluble and insoluble phases following freezing and thawing, a photocatalysis-freeze-thaw circle degradation method of κ-carrageenan has been developed to minimise by-product generation. It was observed that the addition of KCl enhanced the gel strength but could lead to the molecular-weight decrease of the prepared LMWC whose relative molecular weight could reduce to ≤ 2.8 kDa. Moreover, FT-IR, HPLC-MSn, and NMR analysis results showed that the photocatalysis-freeze-thaw circle method could separate the degraded LMWC in time to avoid the multiple reaction during the reaction process, which can fully protect the sulfate groups of LMWC from further degradation and produce less by-products. In addition, the immunomodulatory effects of carrageenan oligosaccharides in immunocompromised mice were investigated through whole blood assays, H&E staining, immunohistochemistry, and targeted metabolomics. The results indicated that carrageenan oligosaccharides could repair damage to immune organs, maintain tissue structural integrity, promote the generation and proliferation of T cells (CD4⁺, CD8⁺), and stimulate antibody (IgA, IgM) secretion. Concurrently, it could reverse intestinal metabolic dysregulation and restore gut metabolic pathways. The present study provides insight for the development of immunomodulatory functional oligosaccharides.