Fluorinated polyurethaneimide (PUI) electro-optic waveguide polymer with polyurethane and polyimide chain segment structures was synthesized by stepwise polymerization using the synthesized amino ester oligomer pu and imide oligomer pi as monomers. Since the main chain structure of the synthesized PUI had the functionality of both polyurethane and polyimide chain segment structures, it combines the excellent thermal and film-forming properties of polyurethanes and polyimides, as well as lower optical transmission loss in the near-infrared wavelength band. The glass transition temperature (Tg) of PUI was 182 °C, and the 5% heat loss decomposition temperature was 325 °C. The PUI had good optical properties with an optical propagation loss of 1.10 dB/cm and an electro-optic (EO) coefficient (γ33) of 86 pm/V at a wavelength of 1550 nm. A Mach-Zehnder interferometric polymer waveguide EO modulator had been designed and fabricated by using the PUI as a waveguide electro-optic core layer. The prepared polymer waveguide EO modulator showed a good electro-optic modulation response at a wavelength of 1550 nm under an applied 1 kHz sinusoidal modulation signal. The results showed that the synthesized PUI met the performance requirements for the preparation of polymer optical waveguide devices and was a polymer electro-optic waveguide material with good overall performance.