Fluid catalytic cracking (FCC) unit emits a large amount of flue gas, which is a major concern of environmental protection supervision. Wet flue gas desulfurization (WFGD) technologies have been widely used to control the emissions of SO2 in refineries. In this study, stack tests for pollutants emission of a typical FCC unit were conducted. The emission characteristics of the FCC unit indicated that WFGD would cause a large amount of water vapor in the flue gas, which indirectly leads to large quantities of salt pollutants entrained in the flue gas including ammonium sulfite ((NH4)2SO3) and ammonium sulfate ((NH4)2SO4). A strong correlation among the concentrations of SO2, NH3, and H2O was observed, and factor analysis shows that these concentrations are dominated by a common factor. It was also found that a mass quantity of NH4+ and SO32− existed in the condensate water of the flue gas. The TG-MS analysis shows that (NH4)2SO3 could be decomposed at 94.1 °C, and NH3, SO2, and H2O are released as reaction products in the form of gas. Therefore, a part of the NH3 and SO2 obtained by Fourier transform infrared spectroscopy (FTIR) monitoring may be derived from the decomposition of (NH4)2SO3 in the flue gas due to the high temperature during the sampling process, which was also confirmed in a lab experiment. The hot and wet sampling process will lead to overestimation of NH3 and SO2 emissions rather than FTIR method itself when monitoring the high-humidity FCC flue gas. Thus, the concentration of H2O in the flue gas and the type of sampling process need to be taken into consideration during the monitoring process.