Acetylcholinesterase (AChE) inhibition enhances learning and cognitive ability for treatment of Alzheimer's disease. Polysaccharide–peptide complexes were identified in Cordyceps militaris (CPSPs) and characterized for their AChE inhibitory properties. Three polymers (CPSP-F1, -F2, and -F3) were extracted and separated by ultrasound-assisted extraction and diethylaminoethanol (DEAE)–Sepharose CL-6B column chromatography. Polysaccharide–peptide complexes were identified by DEAE–Sepharose CL-6B column chromatography and high-performance gel-filtration chromatography, Fourier transform infrared spectra, amino sugar composition analysis, and β-elimination reaction to identify polysaccharide–peptide bond categories. Separation of CPSP can increase AChE inhibitory activity from the crude polysaccharide of C. militaris. CPSP-F1 and CPSP-F2 exhibited half maximal inhibitory concentrations of 32.2 ± 0.2 mg/mL and 5.3 ± 0.0 mg/mL. Thus, we identified polysaccharide–peptide complexes from C. militaris and suggest CPSP has great potential in AChE inhibition bioassay.