Polyurethane elastomers (PUEs) based on poly(2-ethyl-1,3-hexamethylene adipate) glycol (PEHA), poly(2,4-diethyl-1,5-pentamethylene adipate) glycol (PDEPA) and poly(2-butyl-2-ethyl-1,3-trimethylene adipate) glycol (PBETA) were synthesized with 4,4'-diphenylmethane diisocyanate (MDI) and 1,4-butane diol (BD)/1,1,1-trimethylol propane (TMP). PEHA has one primary and one secondary hydroxyl groups, but PDEPA or PBETA has two primary hydroxyl groups. The effect of low reactive secondary OH group on molecular aggregation structure and mechanical properties of the PUEs was investigated using Fourier transform infrared spectroscopy (FT-IR), differential scanning calorimetry (DSC), small-angle X-ray scattering (SAXS), dynamic viscoelastic measurement and tensile testing. The study demonstrates that PEHA-based PUE has lower cross-linking density and lower degree of microphase separation than PDEPA- and PBETA-based PUEs. As a result, PEHA-based PUE has lower dynamic storage modulus value at the rubbery plateau region and Young's modulus. (C) 2017 Elsevier Ltd. All rights reserved.