A β-cyclodextrin (β-CD)-bonded gel monolithic column polydimethylsiloxane (PDMS) microfluidic device was developed in a simple and feasible way. Before preparation of gel monolithic column in PDMS microchannel, PDMS surface was activated by UV light to create silanol groups, which is an active molecule to covalently bond 3-(trimethoxysilyl)-propyl methacrylate (Bind-Silane) and seal microfluidic device. By the way, Bind-Silane is a bifunctional molecule to link polyacrylamide (PAA) gel and inner wall of PDMS microchannel covalently. Allyl-β-CD was used not only as a multifunctional crosslinker in PAA gel to control the size of the pores, but also as a chiral selector for the enantioseparation. The stability, transferring heat and optical characteristic of the microfluidic device were examined. The separation capability of the gel monolithic column was confirmed by the successful separation of fluorescein isothiocyanate (FITC)-labeled arginine (Arg), glutamine acid (Glu), tryptophan (Try), cysteine (Cysteine) and phenylalanine (Phe) in the PDMS microfluidic device less than 100 s at 36 mm effective separation length. A maximum of 2.06 × 10 5 theoretical plates was obtained by the potential strength of 490 V/cm. A pair of FITC-labeled dansyl- d, l-threonine (Dns-Thr) was separated absolutely.