Low-molecular-weight exopolysaccharides of Cordyceps militaris (LCMP), obtained by enzymatically digesting the exopolysaccharide produced by C. militaris, were purified and found to be comprised of 77.9% mannose and 22.1% glucose. Additionally, lactic acid bacteria (LAB) strains, including Enterococcus faecalis strain L4, Pediococcus acidilactici strain L25, and Companilactobacillus zhachilii strain L113, were isolated and their growth phenotypes and metabolites appeared in the presence or absence of purified LCMP were determined. In medium containing purified LCMP with low glucose, strains L4, L25, and L113 all exhibited auto-aggregation; however, co-aggregation occurred only with the strain L113. Moreover, culture media of strains L4, L25, and L113 in either the presence or the absence of LCMP could all inhibit the growth of pathogenic bacteria. Culture media of strains L4, L25, and L113 with purified LCMP contained higher concentrations of lactic acid and other organic acids than in media cultured without purified LCMP. Additionally, the proliferation of HT-29 cells was more effectively inhibited by culture media of strains L4, L25, and L113 with purified LCMP. Together, these results indicated that LCMP may provide positive effects for the host by promoting probiotics to inhibit the growth of pathogens and increase the production of metabolites related to anticancer activity.