High salinity has attracted much attention because of its serious effects on functional microorganisms during wastewater treatment. Most of the research on salt stress has investigated the impacts on individual nitrification or denitrification by controlling the total salinity of wastewater. However, the effects and mechanisms of the ion composition on simultaneous nitrification and denitrification (SND) are poorly understood under salt stress. Na+ and K+ are important components of salt stress because of their high contents and difficult removal characteristics from wastewater. This study systematically investigated the individual and combined effects of Na+ and K+ on SND using continuous tests with the increasing salinity. Compared with the control, K+ and combined stresses had no effects on nitrogen transformation and removal within 2.86% salinity. However, Na+ stress decreased ammonia nitrogen (NH4+-N) removal and caused the serious nitrite nitrogen (NO2–-N) accumulation at 2.36% and 2.86% salinities. Moreover, Na+ stress significantly enhanced narH expression and the relative abundance of denitrifying bacteria, especially Ottowia at 2.86% salinity. Na+ stress results in an out-of-synch problem between NO2–-N production and consumption by destroying the balance of the bacterial community. This study indicates that Na+ concentration and accumulation should be considered in the SND for nitrogen removal.