In this study, polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) and polychlorinated naphthalenes (PCNs) in stack gas of waste incinerators were monitored by using high resolution gas chromatography-high resolution mass spectrometry (HRGC/HRMS) with isotope internal standard dilution method. Emissions characteristics and correlation of the two groups' pollutants were also discussed, which could provide helpful theoretical foundation for controlling PCDD/Fs and PCNs emissions from organized sources. The results showed that, (1) no obvious PCDD/Fs or PCNs contamination was found in blank experiments; (2) the recoveries of the added internal standard for sampling and extracting satisfied the requirements of US EPA23 and CHN HJ77.2-2008, which were 74.0%~90.1% and 53.3%~120.0%, respectively; (3)for PCDD/Fs, the concentration of homologues were increased with the increase of the chloride numbers, while for PCNs, the homologues firstly increased then decreased with the increase of the chloride numbers. In addition, the Pearson correlation coefficients of the adjacent homologues of both PCDD/Fs and PCNs were higher than that of the non-adjacent ones, which may reveal that the chlorination of low chlorinated homologues was an important pathway of the formation of higher chlorinated ones. High linear correlation were found from some PCNs (i.e., PeCN, HxCN, HpCN and OCN) and some PCDD/Fs (i.e., OCDD, PeCDF, HxCDF and HpCDF) (R²=0.55~0.78), which may suggest similar formation mechanism of these homologues during the process of waste incineration.