Polytetrafluoroethylene has broad application prospects and great potential value in the field of photonic crystal substrate materials because of its low dielectric constant and low loss of light transmission at 0.7-2.5 THz. This paper describes the use of femtosecond laser, with a pulse duration of 388 fs and repetition frequency of 100 kHz, to research the preparation of two-dimensional photonic crystal from polytetrafluoroethylene sheet. By fitting the experimental results, the calculated radiation exposure was found to be 840 mJ/cm² at wavelength of 1040 nm. In addition, it was revealed that laser parameters affected the quality of the two-dimensional photonic crystal and the single-layer micropore processing quality under the multi-pulse tapping path were the best. Further, the effects of laser power, scanning speed, and scanning times on the periodic cylindrical structure were investigated. Desirable preparing results were obtained at an average laser power of 9 W, scanning speed of 100 mm/s, and scanning times of 9. The results of this study can be useful for preparing two-dimensional photonic crystal of polytetrafluoroethylene by ultrafast laser.