Nitrogen exists in municipal wastewater in the form of ammonia/ammonium which is a recoverable resource. Recovering nitrogen to improve nitrogen-use efficiency should be carefully considered to promote global environmental sustainability. However, ammonia/ammonium is always not well recovered but removed as one of the main pathways for nitrogen release into the environment, which is due to ineffective ammonia capture. In this study, a new method of ion-exchange resin ammonium recovery combined with membrane capacitive deionization (MCDI + IE process) pretreatment is proposed. Selective ion removal by MCDI is demonstrated and ammonium ratio to the total prior ion (K+, Ca2+ and Mg2+) in outflow of MCDI cell is respectively increased from ∼15% to over 30% and 45% after 3 and 5 MCDI cycles. The MCDI + IE process could deal with 2.48 and 3.89 times of inflow, respectively, compared with the single IE process after 3 and 5 MCDI charge–discharge cycles and recover more than 65% of ammonium in a resin regeneration cycle after 3 MCDI cycles. It ascribes to MCDI desalination eliminating the negative effects of divalent cations, such as Ca2+ and Mg2+, on the IE absorb–desorb process.