The surface chemistry reaction involved in the processing of Atmospheric Pressure Plasma Jet (APPJ) produced from CF4 precursor has been explored. The atomic emission spectroscopy of F atoms and CF2 molecules was investigated as they contribute to substrate etching and FC film formation during APPJ processing. Optical emission spectroscopy (OES) spectra were acquired for CF4 plasma, relative concentrations of excited state species of F atoms and CF2 molecules were also dependent upon plasma parameters. The densities of F atoms increased dramatically with increasing applied RF power, whereas CF2 molecules decreased monotonically over the same power range, the subsequent electron impacted decomposition of plasma species after CF4 precursor fragmentation. The spectrum of the F atoms and CF2 molecules fallowed the same tendency with the increasing concentration of gas CF4, reaching the maximum at the 20sccm and 15sccm respectively, and then the emission intensity of reactive atoms decreased with more CF4 molecules participating. Addition certain amount O2 into CF4 plasma resulted in promoting CF4 dissociation, O2 can easily react with the dissociation product of CF2 molecules, which inhibit the compound of the F atoms, so with the increasing concentration of O2, the concentration of the CF2 molecules decreased and the emission intensities of F atoms showed the maximum at the O2/CF4 ratio of 20%. These results have led to the development of a scheme that illustrates the mechanisms of surface chemistry reaction and the affection of plasma parameters in CF4 plasma systems with respect to F and CF2 gas-phase species.