Some thermal stable fluorine-containing polyimides with side-chain second-order nonlinear optical (NLO) chromophores have been developed, which were prepared by one preimidized, hydroxyl polyimide, followed by the covalent bonding of a chromophore onto the backbone of the polyimide via the Mitsunobu condensation, and the chromophore loading level in the polyimide was controlled efficiently by weight percent. Detailed physical properties showed that the resulting polyimides have good solubility in common organic solvents, relative high glass transition temperatures. Polymer waveguide devices can be easily spin-coated, ensuring a long-term alignment stability at elevated temperatures. These devices exhibit large electro-optic coefficients, 25 pm V-1 at 0.83 mum, which retained > 95% at 120 degreesC for more than 100 h.