Nitrogen removal is an obstacle for the wide application of wastewater ecological soil infiltration (WESI) system in domestic wastewater treatment. In this study, matrix dissolved oxygen (DO), nitrogen removal and nitrous oxide (N2O) emission in aerated pilot WESI systems were investigated under different aeration times (1, 2, 3, 4 and 6 h/d) and aeration rates (1, 2, 3 and 4 L/min). The results showed that aerobic conditions in upper matrix and anoxic or anaerobic conditions in the subsequent matrix were developed in an aerated/non-aerated cycle at the optimal aeration condition of aeration time of 4 h/d and aeration rate of 3 L/min. Simultaneously, high removal efficiency of chemical oxygen demand (COD) (97.9%), NH4+-N (98.2%), total nitrogen (TN) (90.7%) and low N2O emission rate (13.2 mg/(m2 d)) were obtained. The results would provide optimal aeration parameters for application of intermittent aerated WESI systems.