The effects of salinity changes on nitrogen transformation efficiency and recoverability were studied by using a partial nitration (PN)-anaerobic ammonium oxidation (Anammox) integrated reactor. The changes of microbial community structure and population abundance during the increase and decrease of salinity were also analyzed by 16S rRNA gene high-throughput sequencing. The results showed that when the salinity was increased to 1.35%, the combined PN-Anammox process achieved the maximum stimulated and total nitrogen removal rate (TNRR) arrived at 1.1 kg/(m(3).d). When the salinity was higher than 1.35%, the activities of AOB and Anammox bacteria began to be inhibited. When the salinity reached 2.4%, the TNRR decreased to 60%. TNRR was fast restored, when salinity was reduced to 0.11%. The genes of AOB and Anammox bacteria indicated that the TNRR of the reactor was restored after salinity inhibition, but the functional microbial community structure and abundance had relatively large, irreversible changes.