The microstructure development of 4,4'-diphenylmethane diisocyanate (MDI) and 1,4-butanediol (BDO) based thermoplastic polyurethane (TPU) under compression was investigated. Influential factors on the permanent compression deformation were discussed in detail. Two types of samples with the same chemical compositions while different aggregation structures were prepared by altering the stirring speed during the synthesis process. The difference in the first-order structure of these samples was studied by C-13 NMR. The aggregation structures and the corresponding development under compression were characterized by DSC, WAXD and SAXS, respectively. These observed results indicated that difference of microstructures lead to different deformation behaviors, and the disruption of hard segment domains or reorganized structures by less ordered hard segments played significant roles in the permanent deformation under compression. The viscoelastic behaviors of these samples were described by DMA and simulated by Rouse model. The derived terminal viscosity and relaxation times were used to explain the different permanent deformations of these samples. Finally, an optimized micro-crosslink structure was introduced in TPUs, and a better deformation resistance property was obtained. Crown Copyright (C) 2012 Published by Elsevier Ltd. All rights reserved.