A method for treating wastewater containing TMAH and ammonium nitrogen includes the steps of (a) introducing a first solution which contains ammonium nitrogen but no TMAH into a single reactor with microorganisms comprising nitrifying bacteria and anammox bacteria, and denitrifying the first solution by the microorganisms under a dissolved oxygen concentration ranging from 0.1-0.5 mg/L and a pH value of 7-8; (b) when the denitrification efficiency reaches a steady state, introducing a second solution which contains ammonium nitrogen and TMAH and has a concentration of TMAH lower than 60 mg/L into the reactor; and (c) gradually increasing the concentration of TMAH in the solution to be added into the reactor for several times whenever the denitrification efficiency reaches a steady state. Accordingly, the inhibition of TMAH to the anammox bacteria can be significantly decreased, and both TMAH and the ammonium nitrogen can be treated simultaneously.