To better understand the structure-function relationship of Gastrodia elata polysaccharides (PGEs), PGEs were extracted by ultrasound-assisted extraction method and the effects of extraction time on the structure and conformation of PGEs were evaluated by asymmetrical flow field-flow fractionation (AF4) coupled online with multiangle light scattering (MALS) and differential refractive index (dRI) detectors (AF4-MALS-dRI). Besides separation, AF4-MALS-dRI can provide more information about PGEs, such as size and molecular weight (Mw) distributions, apparent density, and conformation. The effects of PGEs on the proliferation, apoptosis, and cell cycle of MCF-7 cells were investigated. The cell activity assay indicated that the PGEs can inhibit the growth of MCF-7 cells by inducing late apoptosis. The results indicated that PGEs with a spherical conformation and compact structure seem to be beneficial to inducing MCF-7 cells late apoptosis. Moreover, results demonstrated that the information obtained by AF4-MALS-dRI is valuable for better understanding of the relationship of structure-activity of PGEs.