Five iridoid glycosides were prepared using molecularly imprinted solid-phase extraction combined with preparative high-performance liquid chromatography. Hydrophilic molecularly imprinted polymers were synthesized using α-1-allyl-2-N-acetyl glucosamine, which introduced an abundance of hydrophilic groups into the polymers. Using molecularly imprinted solid-phase extraction as the sample pretreatment procedure, five iridoid glycosides, gardenoside, geniposide, shanzhiside, geniposidic acid, and genipin-1-O-gentiobioside, were selectively enriched from Gardenia fructus extracts. Preparative high-performance liquid chromatography then provided iridoid glycosides with a purity >98%. The structures were elucidated by using nuclear magnetic resonance spectroscopy, optical rotation and melting point measurements, and mass spectrometry. The results demonstrate that molecularly imprinted solid-phase extraction combined with preparative high-performance liquid chromatography was an efficient, rapid, and economical method for the preparation of bioactive compounds from natural products.