Understanding of the main factors affecting the hydrothermal stability of zeolites is vital for the application of zeolites in catalysis and separation. Although incorporation of extra-framework metal cations is an important stagey to improve the hydrothermal stability of Al-rich zeolites, how these metal cations affect the hydrothermal stability of high-silica zeolites is not well understood. In this work, the effects of residual alkali cations on the hydrothermal/thermal stability of silicalite-1, a pure-silica MFI-type zeolite, is explored. We show that the alkali impurities from commercial tetrapropylammonium hydroxide (TPAOH) are not negligible; the concentration and type of residual alkali cations dictate the hydrothermal/thermal stability of silicalite-1. Above a certain concentration (∼0.3–0.5 wt%), the alkali cations can lead to less silanol defects but much poorer hydrothermal/thermal stability. Below this concentration, the degrading effect is negligible. Removal of the alkali cations by proton exchange improves the stability significantly. Steaming (hydrothermal treatment) has two opposite effects on the silicalite-1 crystal structure: destruction by hydrolysis and perfecting by healing the defects. For silicalite-1 with considerable amounts of alkali cations, the destruction effect predominates; while the perfecting effect predominates for silicalite-1 with low alkali contents.