The mineralization of perfluorinated alkyl substances (PFASs) by calcium compounds during the waste thermal treatment was systemically studied. Different calcium compounds showed different mineralization efficiencies of PFASs during the thermal process, owing to the different reaction mechanisms. Calcium hydroxide was recommended as the most effective Ca reagent for PFAS defluorination because the carbon-fluorine bonds in PFASs can be converted to carbon-hydrogen bonds via the hydrodefluorination reaction. PFASs with different chain lengths and functional groups were further investigated for their potentially different mineralization behavior. The results showed that the chain length of PFASs had an insignificant effect on the mineralization efficiency by calcium hydroxide. The thermogravimetric analysis-differential thermal analysis (TGA-DTA) also revealed that perfluorooctanesulfonate (PFOS) and perfluorohexanesulfonate (PFHxS) (with different chain lengths) had a similar thermal behavior. However, PFASs with different functional groups showed different mineralization behavior with calcium hydroxide in relation to their different thermal decomposition temperatures. Finally, the mineralization ratio of polytetrafluoroethylene (PTFE) particles by calcium hydroxide could reach 80% or higher when the temperature was above 400 °C. The gas chromatography/mass spectrometry (GC/MS) results demonstrated much reduced production of gaseous fluorocarbon fragments during PTFE decomposition when coexisting with calcium hydroxide.