A series of poly(methyl(trifluoropropyl)-diphenyl siloxane) (P(MTFPS- co -DPS)) was synthesized by polycondensation of diphenylsilanediol and methyltrifluoropropylsiloxanediol. Their chemical structures were investigated by gel permeation chromatography (GPC), Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), and differential scanning calorimeter (DSC). The effect of diphenylsiloxane (DPS) units on the thermal stability of poly[methyl(trifluoropropyl)siloxane] (PMTFPS) was studied by thermogravimetric analysis (TGA), isothermal degradation tests, and pyrolysis-gas chromatography-mass spectrometry (Py-GCMS). The results showed that the thermal stability of PMTFPS improved with the introduction of DPS units into the chain. In particular, the temperature for 5% mass loss in PMTFPS increased by 72 °C under a nitrogen atmosphere. In addition, the mechanism by which the DPS units improve the thermal stability of PMTFPS was also investigated.