The atmospheric fluorocarbon plasma plays an important role in the surface modification of insulating materials like polymers. The existing fluorocarbon plasma is usually generated by dielectric barrier discharge, which has low concentration of reactive species and may cause insufficient surface fluorination. This work attempts to develop an atmospheric fluorocarbon plasma jet using a coaxial transmission line resonator by microwave discharge with locally enhanced electric field and high density. The gas temperature is reduced by pulse modulation technology. Three kinds of working gases, the pure CF4, Ar/CF4 and He/CF4 are utilized to generate atmospheric microwave fluorocarbon plasma jet. The discharge images, optical emission spectra, electron densities and gas temperatures are studied experimentally. The results show that the Ar/CF4 plasma jet has the best comprehensive performance, like the strong discharge intensity and controllable gas temperature. The electron density of the Ar/CF4 plasma jet is on the magnitude of 1020 m−3, indicating a higher density than that of the frequently used dielectric barrier discharge. With the other conditions unchanged, the gas temperature in the end of Ar/CF4 plasma jet can be reduced from 410.2 to 347.3 K by decreasing the duty cycle of modulated pulse from 0.5 to 0.1. Thence, the microwave Ar/CF4 plasma jet is considered to be a promising fluorocarbon plasma source for surface fluorination of polymers.