The hydrolysis of a newly synthesized polyether urethane (PEU) that uses polydimethylsiloxane (PDMS) as a second macrodiol and fluorinated diol (FDO) as another chain extender has been studied via immersion in buffer solutions at 70 °C. The hydrolysis process was monitored using scanning electron microscopy (SEM), gel permeation chromatography (GPC), and tensile testing. After aging for 32 weeks, no surface defect was observed on the fluorinated silicon-containing PEUs (FSPEU). Meanwhile, the addition of FDO did not alter the other issues of bulk hydrolysis, such as the changes in molecular weight and mechanical strength. Moreover, microphase separation of FSPEU was suppressed during temperature-accelerated hydrolysis, whereas aging induced a more noticeable phase of morphological change in silicon-modified PEUs (SPEU) due to the hindrance effect of the fluorinated side chains. The formation of hydrolysis-prone allophanate is also reduced in the presence of FDO. FSPEU with enhanced antihydrolysis performance can potentially be applied to biostable medical devices.