Fluorinated polyimide materials were selected for their exceptional flexibility, high thermal stability, and minimal absorption loss. These materials were subsequently employed in the production of single-mode polymer optical waveguide devices using photolithography. In this study, a fluorinated polyimide material doped with NaYF4 nanocrystals was prepared and confirmed to exhibit low absorption loss near 1550 nm, which is within the common communication window. The refractive index of the fluorinated polyimide films was precisely adjusted by the NaYF4 doping, the adjustable ranges for the refractive index were 1.95% and 1.72% for doped and undoped, respectively. Secondly, utilizing the NaYF4 nanocrystals doped-fluorinated polyimide materials, a three-layer single-mode polymer optical waveguide device for C-band (near 1550 nm) optical interconnection was fabricated by etching the underlying cladding and employing silicon nitride as a mask. The transmission performance of the device was excellent, with a total waveguide coupling and transmission loss of 1.502 dBm.