Transparent polyimides (PI) films with outstanding overall performance are attractive for next generation optoelectronic and microelectronic applications. Semi-alicyclic PIs derived from alicyclic dianhydrides and aromatic diamines have proved effective to prepare transparent PIs with high transmittance. To optimize the combined properties of semi-alicyclic PIs, incorporating bulky trifluoromethyl groups into the backbones is regarded as a powerful tool. However, the lack of fundamental understanding of structure–property relationships of fluorinated semi-alicyclic PIs constrains the design and engineering of advanced films for such challenging applications. Herein, a series of semi-alicyclic PIs derived from alicyclic dianhydrides and trifluoromethyl-containing aromatic diamines was synthesized by solution polycondensation at high temperature. The effects of alicyclic structures and bulky trifluoromethyl groups on thermal, dielectric and optical properties of PIs were investigated systematically. These PI films had excellent solubility, low water absorption and good mechanical property. They showed high heat resistance with Tg in the range of 294–390 °C. It is noted that tensile strength and thermal stability were greatly affected by the rigid linkages and alicyclic moieties, respectively. These films exhibited obviously low refractive indices and significantly reduced dielectric constants from 2.61 to 2.76, together with low optical birefringence and dielectric anisotropy. Highly transparent films exhibited cutoff wavelength even as low as 298 nm and transmittance at 500 nm over 85%, displaying almost colorless appearance with yellowness index (b*) below 4.2. The remarkable optical improvement should be mainly ascribed to both weak electron-accepting alicyclic units and bulky electron-withdrawing trifluoromethyl or sulfone groups. The present work provides an effective strategy to design molecular structures of optically transparent PIs for a trade-off between solution-processability, low water uptake, good toughness, high heat resistance, low dielectric constant and excellent optical transparency.