The estrogenic compound 17b-estradiol (E2) is widely studied for its potential endocrine disruption effects. Due to the low level of E2 present in the environment, it is highly desirable to develop a sensitive and efficient separation and enrichment method for E2 analysis. In this paper, we proposed a novel E2 preconcentration method using anti-E2 aptamer-anchored isothiocyanate-modified beads (NCS beads). The glass beads are chemically modified with primary amino group, and then treated with phenylene diisothiocyanate (PDITC) to generate an isothiocyanate group, which is reactive towards the amine group. The amino-modified anti-E2 aptamer can be easily covalently immobilized onto the as-prepared NCS beads. The experimental results demonstrated that the aptamer affinity microbeads could selectively retain and separate E2 compound. The effects of the operation parameters on retention of E2, including washing condition, eluting condition, the number of beads, and the incubation time were investigated. Moreover, high-performance liquid chromatography with preconcentration of E2 on the aptamer affinity microbeads was applied to detect the E2 in the spiked water samples and obtained a good recovery.