Since polyurethane elastomer (PUE) is widely used in many fields, it is always the popular topic in the scientific research. In this paper 1,4-butanediol (1,4-BDO), neopentyl glycol (NPG) and bisphenol-a (BPA) were chosen as chain extenders to prepare polyurethane elastomer (PUE) due to their representative structures. After the synthesis of PUE with these comparable chain extenders, morphology and thermal properties were evaluated by different characterization methods The results showed that, compared with NPG and BPA, 1,4-BDO has made PUE in synthesis of para-phenylene (PPDI) more easily crystallize in soft segments while PUE based on diphenyhnethane diisocyanate (MDI) arrange orderly in hard segments, so that micro-phase separation appeared. Besides, PUE in synthesis of PPDI and 1,4-BDO showed the best thermal stability. Additionally, chain extenders increased the viscosity of samples, especially 1,4-BDO, which made PUE not only have a relatively higher viscosity, but also maintain a good process ability.