In order to efficiently remove nutrients from saline wastewater, biological aerated filter systems were designed, set up and operated with synthetic wastewater, in which the concentrations of CODCr, total nitrogen and total phosphorus were respectively in the ranges of 300～400 mg／L, 30～45 mg／L and 3.5～5.5 mg／L. The effect of operational parameters on the removal of organics, nitrogen and phosphorus was investigated. To improve the removal of nitrogen and phosphorus, the aeration mode changed from continuous to intermittent. The enhancement of biofilter performance caused by intermittent aeration was examined and the optimal cycle time of intermittent aeration was determined. Under the optimal operating condition, the removal efficiency of CODCr, total nitrogen and phosphorus were 92.1％, 77.9％ and 70.3％, respectively. The intermittently aerated biological filter showed reasonable salt tolerance and efficiency in nutrients removal from saline wastewater (salinity 0％～3％). The removal of CODCr was less sensitive to salinity than nitrogen and phosphorus removal. In comparison to the other studied biological processes, the intermittently aerated biofilter could efficiently remove nutrients at identical salinity, and consequently had superiority and better application prospect.