The gut-microbiota-targeted prebiotic intervention has been a hot topic in the study of health modulation. To examine the effect of fucoidan supplementation on the health of long-cared elderly subjects (88years ± 3.41) with malnutrition (MNA-SF score ≤ 7), an eight-week randomized, single-blind clinical trial was carried out in a community hospital. The subjects were divided into a test group (TG, n = 45), which received the fucoidan supplementation (1g/d) and a control group (CG, n = 20). Preliminary data on metagenomes, plasma metabolomes, prealbumin, twelve cytokines, and clinical records from six people were analyzed. The results showed that with prebiotic intervention, prealbumin, a sensitive nutrition marker slightly increased. Furthermore, in the test group, there were 42 significantly enriched gut microbial species (t-test, p < 0.05), including multiple beneficial bacteria (Bifidobacterium breve, Roseburia hominis, and Lactobacillus acidipiscis), which positively correlated with Medium-Chain Fatty Acid (MCFA)-associated carnitines (octanoylcarnitine and decanoylcarnitine), and chenodeoxycholic acid. The defecation and neuropsychological activities of the participants in the test group also improved slightly. The preliminary data suggests that fucoidan has the potential to improve metabolism, gut function, and nutrition in elderly people by changing the gut microbiota and enriching beneficial bacteria. A larger sample size analysis is needed for a deeper understanding of the effects and mechanism.