As a folk medicine, Botrychium ternatum has been used for thousands of years in China. In the present work, a water soluble polysaccharide BTp1 was extracted and purified from B. ternatum. Based on the MALDI matrix 3-aminoquinoline-α-cyano-4-hydroxycinnamic acid, the molecular weight of BTp1 was determined to be 11638Da directly. Monosaccharide analysis showed that BTp1 was composed of arabinose (Ara). Combining enzymatic hydrolysis and subsequent MALDI-TOF analysis, a linear backbone of BTp1, consisted of (1→5)-linked α-l-Araf, was inferred quickly. Then according to NMR experiments, the whole structure of BTp1 was established. The repeating unit of BTp1 was deduced as a linear backbone with branches at O-2, O-3 and its neighboring O-2 positions terminated with (1→)-linked α-l-Araf, respectively. The immunomodulatory assay exhibited that BTp1 could significantly enhance the viability and promote the release of NO in RAW 264.7 cells, suggesting that BTp1 could be a potential immunomodulatory agent in pharmacological fields.