This study aimed to examine the in vitro digestion properties and immunomodulatory effects of inulin-type fructans (ALP-1) from Arctium lappa L. on immunosuppressive mice and to explore the underlying mechanisms. The simulated gastrointestinal digestion showed that ALP-1 underwent slight degradation during gastric and intestinal fluid digestion, with most of it reaching the gut as long-chain structures. The administration of ALP-1 effectively improved overall health and regulated immune function according to the spleen index, thymus index, splenic T-lymphocyte subsets, and other immune-related cytokines. Besides, 16S rDNA sequencing, ultra-high-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry, and matrix-assisted laser desorption/ionization mass spectrometry imaging technique revealed fructan-induced changes in gut microbiota composition, metabolic processes, and spatial information of key metabolites. These changes likely contributed to the immunomodulatory effects of ALP-1 in immunosuppressive mice. Therefore, ALP-1 shows promise as an immunomodulator for use in functional foods and nutraceuticals.